Starting phenix.real_space_refine (version: dev) on Sun Apr 10 22:04:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wk6_8856/04_2022/5wk6_8856_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wk6_8856/04_2022/5wk6_8856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wk6_8856/04_2022/5wk6_8856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wk6_8856/04_2022/5wk6_8856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wk6_8856/04_2022/5wk6_8856_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wk6_8856/04_2022/5wk6_8856_neut.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.099 sd= 0.695 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 161663 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "B" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "C" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "D" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "E" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "F" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "G" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "H" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "I" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "J" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "K" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "L" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "M" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "N" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "O" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "P" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "Q" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "R" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "S" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "T" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "U" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "V" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "W" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "X" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "Y" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "Z" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "a" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "c" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "d" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "e" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "f" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "g" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "h" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "i" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "j" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "k" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "l" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "m" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "n" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Chain: "o" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 3943 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 267} Chain breaks: 1 Time building chain proxies: 52.84, per 1000 atoms: 0.33 Number of scatterers: 161663 At special positions: 0 Unit cell: (136.5, 136.5, 341.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 17261 8.00 N 15211 7.00 C 48667 6.00 H 80524 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 100.18 Conformation dependent library (CDL) restraints added in 10.5 seconds 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20992 Finding SS restraints... Secondary structure from input PDB file: 287 helices and 41 sheets defined 74.0% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 99 Processing helix chain 'A' and resid 108 through 126 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL A 390 " --> pdb=" O VAL A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 488 Processing helix chain 'B' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 99 Processing helix chain 'B' and resid 108 through 126 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL B 390 " --> pdb=" O VAL B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 488 Processing helix chain 'C' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 99 Processing helix chain 'C' and resid 108 through 126 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL C 390 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA C 457 " --> pdb=" O ALA C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 488 Processing helix chain 'D' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 99 Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL D 390 " --> pdb=" O VAL D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN D 400 " --> pdb=" O ASP D 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA D 457 " --> pdb=" O ALA D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 488 Processing helix chain 'E' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 99 Processing helix chain 'E' and resid 108 through 126 Processing helix chain 'E' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL E 390 " --> pdb=" O VAL E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA E 457 " --> pdb=" O ALA E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 488 Processing helix chain 'F' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN F 15 " --> pdb=" O SER F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 99 Processing helix chain 'F' and resid 108 through 126 Processing helix chain 'F' and resid 386 through 390 removed outlier: 3.668A pdb=" N VAL F 390 " --> pdb=" O VAL F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA F 457 " --> pdb=" O ALA F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 488 Processing helix chain 'G' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN G 15 " --> pdb=" O SER G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 99 Processing helix chain 'G' and resid 108 through 126 Processing helix chain 'G' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL G 390 " --> pdb=" O VAL G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN G 400 " --> pdb=" O ASP G 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN G 407 " --> pdb=" O ALA G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA G 457 " --> pdb=" O ALA G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 488 Processing helix chain 'H' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN H 15 " --> pdb=" O SER H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 99 Processing helix chain 'H' and resid 108 through 126 Processing helix chain 'H' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL H 390 " --> pdb=" O VAL H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN H 400 " --> pdb=" O ASP H 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN H 407 " --> pdb=" O ALA H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA H 457 " --> pdb=" O ALA H 453 " (cutoff:3.500A) Processing helix chain 'H' and resid 478 through 488 Processing helix chain 'I' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN I 15 " --> pdb=" O SER I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 99 Processing helix chain 'I' and resid 108 through 126 Processing helix chain 'I' and resid 386 through 390 removed outlier: 3.668A pdb=" N VAL I 390 " --> pdb=" O VAL I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN I 400 " --> pdb=" O ASP I 396 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN I 407 " --> pdb=" O ALA I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA I 457 " --> pdb=" O ALA I 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 488 Processing helix chain 'J' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN J 15 " --> pdb=" O SER J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 99 Processing helix chain 'J' and resid 108 through 126 Processing helix chain 'J' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL J 390 " --> pdb=" O VAL J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN J 400 " --> pdb=" O ASP J 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN J 407 " --> pdb=" O ALA J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA J 457 " --> pdb=" O ALA J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 478 through 488 Processing helix chain 'K' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN K 15 " --> pdb=" O SER K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 99 Processing helix chain 'K' and resid 108 through 126 Processing helix chain 'K' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL K 390 " --> pdb=" O VAL K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN K 400 " --> pdb=" O ASP K 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN K 407 " --> pdb=" O ALA K 403 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA K 457 " --> pdb=" O ALA K 453 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 488 Processing helix chain 'L' and resid 11 through 35 removed outlier: 3.936A pdb=" N GLN L 15 " --> pdb=" O SER L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 99 Processing helix chain 'L' and resid 108 through 126 Processing helix chain 'L' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL L 390 " --> pdb=" O VAL L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 394 through 449 removed outlier: 3.551A pdb=" N ASN L 400 " --> pdb=" O ASP L 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN L 407 " --> pdb=" O ALA L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA L 457 " --> pdb=" O ALA L 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 478 through 488 Processing helix chain 'M' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN M 15 " --> pdb=" O SER M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 99 Processing helix chain 'M' and resid 108 through 126 Processing helix chain 'M' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL M 390 " --> pdb=" O VAL M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN M 407 " --> pdb=" O ALA M 403 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA M 457 " --> pdb=" O ALA M 453 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 488 Processing helix chain 'N' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN N 15 " --> pdb=" O SER N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 99 Processing helix chain 'N' and resid 108 through 126 Processing helix chain 'N' and resid 386 through 390 removed outlier: 3.670A pdb=" N VAL N 390 " --> pdb=" O VAL N 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN N 400 " --> pdb=" O ASP N 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN N 407 " --> pdb=" O ALA N 403 " (cutoff:3.500A) Processing helix chain 'N' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA N 457 " --> pdb=" O ALA N 453 " (cutoff:3.500A) Processing helix chain 'N' and resid 478 through 488 Processing helix chain 'O' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN O 15 " --> pdb=" O SER O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 99 Processing helix chain 'O' and resid 108 through 126 Processing helix chain 'O' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL O 390 " --> pdb=" O VAL O 387 " (cutoff:3.500A) Processing helix chain 'O' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN O 400 " --> pdb=" O ASP O 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN O 407 " --> pdb=" O ALA O 403 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA O 457 " --> pdb=" O ALA O 453 " (cutoff:3.500A) Processing helix chain 'O' and resid 478 through 488 Processing helix chain 'P' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN P 15 " --> pdb=" O SER P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 99 Processing helix chain 'P' and resid 108 through 126 Processing helix chain 'P' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL P 390 " --> pdb=" O VAL P 387 " (cutoff:3.500A) Processing helix chain 'P' and resid 394 through 449 removed outlier: 3.553A pdb=" N ASN P 400 " --> pdb=" O ASP P 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN P 407 " --> pdb=" O ALA P 403 " (cutoff:3.500A) Processing helix chain 'P' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA P 457 " --> pdb=" O ALA P 453 " (cutoff:3.500A) Processing helix chain 'P' and resid 478 through 488 Processing helix chain 'Q' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN Q 15 " --> pdb=" O SER Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 99 Processing helix chain 'Q' and resid 108 through 126 Processing helix chain 'Q' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL Q 390 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) Processing helix chain 'Q' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN Q 400 " --> pdb=" O ASP Q 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN Q 407 " --> pdb=" O ALA Q 403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA Q 457 " --> pdb=" O ALA Q 453 " (cutoff:3.500A) Processing helix chain 'Q' and resid 478 through 488 Processing helix chain 'R' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN R 15 " --> pdb=" O SER R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 99 Processing helix chain 'R' and resid 108 through 126 Processing helix chain 'R' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL R 390 " --> pdb=" O VAL R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN R 400 " --> pdb=" O ASP R 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN R 407 " --> pdb=" O ALA R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA R 457 " --> pdb=" O ALA R 453 " (cutoff:3.500A) Processing helix chain 'R' and resid 478 through 488 Processing helix chain 'S' and resid 11 through 35 removed outlier: 3.936A pdb=" N GLN S 15 " --> pdb=" O SER S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 99 Processing helix chain 'S' and resid 108 through 126 Processing helix chain 'S' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL S 390 " --> pdb=" O VAL S 387 " (cutoff:3.500A) Processing helix chain 'S' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN S 400 " --> pdb=" O ASP S 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN S 407 " --> pdb=" O ALA S 403 " (cutoff:3.500A) Processing helix chain 'S' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA S 457 " --> pdb=" O ALA S 453 " (cutoff:3.500A) Processing helix chain 'S' and resid 478 through 488 Processing helix chain 'T' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN T 15 " --> pdb=" O SER T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 99 Processing helix chain 'T' and resid 108 through 126 Processing helix chain 'T' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL T 390 " --> pdb=" O VAL T 387 " (cutoff:3.500A) Processing helix chain 'T' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN T 400 " --> pdb=" O ASP T 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN T 407 " --> pdb=" O ALA T 403 " (cutoff:3.500A) Processing helix chain 'T' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA T 457 " --> pdb=" O ALA T 453 " (cutoff:3.500A) Processing helix chain 'T' and resid 478 through 488 Processing helix chain 'U' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN U 15 " --> pdb=" O SER U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 99 Processing helix chain 'U' and resid 108 through 126 Processing helix chain 'U' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL U 390 " --> pdb=" O VAL U 387 " (cutoff:3.500A) Processing helix chain 'U' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN U 400 " --> pdb=" O ASP U 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN U 407 " --> pdb=" O ALA U 403 " (cutoff:3.500A) Processing helix chain 'U' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA U 457 " --> pdb=" O ALA U 453 " (cutoff:3.500A) Processing helix chain 'U' and resid 478 through 488 Processing helix chain 'V' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN V 15 " --> pdb=" O SER V 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 99 Processing helix chain 'V' and resid 108 through 126 Processing helix chain 'V' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL V 390 " --> pdb=" O VAL V 387 " (cutoff:3.500A) Processing helix chain 'V' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN V 400 " --> pdb=" O ASP V 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN V 407 " --> pdb=" O ALA V 403 " (cutoff:3.500A) Processing helix chain 'V' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA V 457 " --> pdb=" O ALA V 453 " (cutoff:3.500A) Processing helix chain 'V' and resid 478 through 488 Processing helix chain 'W' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN W 15 " --> pdb=" O SER W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 99 Processing helix chain 'W' and resid 108 through 126 Processing helix chain 'W' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL W 390 " --> pdb=" O VAL W 387 " (cutoff:3.500A) Processing helix chain 'W' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN W 400 " --> pdb=" O ASP W 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN W 407 " --> pdb=" O ALA W 403 " (cutoff:3.500A) Processing helix chain 'W' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA W 457 " --> pdb=" O ALA W 453 " (cutoff:3.500A) Processing helix chain 'W' and resid 478 through 488 Processing helix chain 'X' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN X 15 " --> pdb=" O SER X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 99 Processing helix chain 'X' and resid 108 through 126 Processing helix chain 'X' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL X 390 " --> pdb=" O VAL X 387 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN X 400 " --> pdb=" O ASP X 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN X 407 " --> pdb=" O ALA X 403 " (cutoff:3.500A) Processing helix chain 'X' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA X 457 " --> pdb=" O ALA X 453 " (cutoff:3.500A) Processing helix chain 'X' and resid 478 through 488 Processing helix chain 'Y' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN Y 15 " --> pdb=" O SER Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 99 Processing helix chain 'Y' and resid 108 through 126 Processing helix chain 'Y' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL Y 390 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) Processing helix chain 'Y' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN Y 400 " --> pdb=" O ASP Y 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN Y 407 " --> pdb=" O ALA Y 403 " (cutoff:3.500A) Processing helix chain 'Y' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA Y 457 " --> pdb=" O ALA Y 453 " (cutoff:3.500A) Processing helix chain 'Y' and resid 478 through 488 Processing helix chain 'Z' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN Z 15 " --> pdb=" O SER Z 11 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 99 Processing helix chain 'Z' and resid 108 through 126 Processing helix chain 'Z' and resid 386 through 390 removed outlier: 3.668A pdb=" N VAL Z 390 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) Processing helix chain 'Z' and resid 394 through 449 removed outlier: 3.551A pdb=" N ASN Z 400 " --> pdb=" O ASP Z 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN Z 407 " --> pdb=" O ALA Z 403 " (cutoff:3.500A) Processing helix chain 'Z' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA Z 457 " --> pdb=" O ALA Z 453 " (cutoff:3.500A) Processing helix chain 'Z' and resid 478 through 488 Processing helix chain 'a' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN a 15 " --> pdb=" O SER a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 99 Processing helix chain 'a' and resid 108 through 126 Processing helix chain 'a' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL a 390 " --> pdb=" O VAL a 387 " (cutoff:3.500A) Processing helix chain 'a' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN a 400 " --> pdb=" O ASP a 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN a 407 " --> pdb=" O ALA a 403 " (cutoff:3.500A) Processing helix chain 'a' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA a 457 " --> pdb=" O ALA a 453 " (cutoff:3.500A) Processing helix chain 'a' and resid 478 through 488 Processing helix chain 'b' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN b 15 " --> pdb=" O SER b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 99 Processing helix chain 'b' and resid 108 through 126 Processing helix chain 'b' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL b 390 " --> pdb=" O VAL b 387 " (cutoff:3.500A) Processing helix chain 'b' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN b 400 " --> pdb=" O ASP b 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN b 407 " --> pdb=" O ALA b 403 " (cutoff:3.500A) Processing helix chain 'b' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA b 457 " --> pdb=" O ALA b 453 " (cutoff:3.500A) Processing helix chain 'b' and resid 478 through 488 Processing helix chain 'c' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 99 Processing helix chain 'c' and resid 108 through 126 Processing helix chain 'c' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL c 390 " --> pdb=" O VAL c 387 " (cutoff:3.500A) Processing helix chain 'c' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN c 400 " --> pdb=" O ASP c 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN c 407 " --> pdb=" O ALA c 403 " (cutoff:3.500A) Processing helix chain 'c' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA c 457 " --> pdb=" O ALA c 453 " (cutoff:3.500A) Processing helix chain 'c' and resid 478 through 488 Processing helix chain 'd' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN d 15 " --> pdb=" O SER d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 99 Processing helix chain 'd' and resid 108 through 126 Processing helix chain 'd' and resid 386 through 390 removed outlier: 3.668A pdb=" N VAL d 390 " --> pdb=" O VAL d 387 " (cutoff:3.500A) Processing helix chain 'd' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN d 400 " --> pdb=" O ASP d 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN d 407 " --> pdb=" O ALA d 403 " (cutoff:3.500A) Processing helix chain 'd' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA d 457 " --> pdb=" O ALA d 453 " (cutoff:3.500A) Processing helix chain 'd' and resid 478 through 488 Processing helix chain 'e' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN e 15 " --> pdb=" O SER e 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 99 Processing helix chain 'e' and resid 108 through 126 Processing helix chain 'e' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL e 390 " --> pdb=" O VAL e 387 " (cutoff:3.500A) Processing helix chain 'e' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN e 400 " --> pdb=" O ASP e 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN e 407 " --> pdb=" O ALA e 403 " (cutoff:3.500A) Processing helix chain 'e' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA e 457 " --> pdb=" O ALA e 453 " (cutoff:3.500A) Processing helix chain 'e' and resid 478 through 488 Processing helix chain 'f' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN f 15 " --> pdb=" O SER f 11 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 99 Processing helix chain 'f' and resid 108 through 126 Processing helix chain 'f' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL f 390 " --> pdb=" O VAL f 387 " (cutoff:3.500A) Processing helix chain 'f' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN f 400 " --> pdb=" O ASP f 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN f 407 " --> pdb=" O ALA f 403 " (cutoff:3.500A) Processing helix chain 'f' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA f 457 " --> pdb=" O ALA f 453 " (cutoff:3.500A) Processing helix chain 'f' and resid 478 through 488 Processing helix chain 'g' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 99 Processing helix chain 'g' and resid 108 through 126 Processing helix chain 'g' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL g 390 " --> pdb=" O VAL g 387 " (cutoff:3.500A) Processing helix chain 'g' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN g 400 " --> pdb=" O ASP g 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN g 407 " --> pdb=" O ALA g 403 " (cutoff:3.500A) Processing helix chain 'g' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA g 457 " --> pdb=" O ALA g 453 " (cutoff:3.500A) Processing helix chain 'g' and resid 478 through 488 Processing helix chain 'h' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) Processing helix chain 'h' and resid 44 through 99 Processing helix chain 'h' and resid 108 through 126 Processing helix chain 'h' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL h 390 " --> pdb=" O VAL h 387 " (cutoff:3.500A) Processing helix chain 'h' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN h 400 " --> pdb=" O ASP h 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN h 407 " --> pdb=" O ALA h 403 " (cutoff:3.500A) Processing helix chain 'h' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA h 457 " --> pdb=" O ALA h 453 " (cutoff:3.500A) Processing helix chain 'h' and resid 478 through 488 Processing helix chain 'i' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 99 Processing helix chain 'i' and resid 108 through 126 Processing helix chain 'i' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL i 390 " --> pdb=" O VAL i 387 " (cutoff:3.500A) Processing helix chain 'i' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN i 400 " --> pdb=" O ASP i 396 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN i 407 " --> pdb=" O ALA i 403 " (cutoff:3.500A) Processing helix chain 'i' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA i 457 " --> pdb=" O ALA i 453 " (cutoff:3.500A) Processing helix chain 'i' and resid 478 through 488 Processing helix chain 'j' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN j 15 " --> pdb=" O SER j 11 " (cutoff:3.500A) Processing helix chain 'j' and resid 44 through 99 Processing helix chain 'j' and resid 108 through 126 Processing helix chain 'j' and resid 386 through 390 removed outlier: 3.668A pdb=" N VAL j 390 " --> pdb=" O VAL j 387 " (cutoff:3.500A) Processing helix chain 'j' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN j 400 " --> pdb=" O ASP j 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN j 407 " --> pdb=" O ALA j 403 " (cutoff:3.500A) Processing helix chain 'j' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA j 457 " --> pdb=" O ALA j 453 " (cutoff:3.500A) Processing helix chain 'j' and resid 478 through 488 Processing helix chain 'k' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) Processing helix chain 'k' and resid 44 through 99 Processing helix chain 'k' and resid 108 through 126 Processing helix chain 'k' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL k 390 " --> pdb=" O VAL k 387 " (cutoff:3.500A) Processing helix chain 'k' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN k 400 " --> pdb=" O ASP k 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN k 407 " --> pdb=" O ALA k 403 " (cutoff:3.500A) Processing helix chain 'k' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA k 457 " --> pdb=" O ALA k 453 " (cutoff:3.500A) Processing helix chain 'k' and resid 478 through 488 Processing helix chain 'l' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) Processing helix chain 'l' and resid 44 through 99 Processing helix chain 'l' and resid 108 through 126 Processing helix chain 'l' and resid 386 through 390 removed outlier: 3.668A pdb=" N VAL l 390 " --> pdb=" O VAL l 387 " (cutoff:3.500A) Processing helix chain 'l' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN l 400 " --> pdb=" O ASP l 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN l 407 " --> pdb=" O ALA l 403 " (cutoff:3.500A) Processing helix chain 'l' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA l 457 " --> pdb=" O ALA l 453 " (cutoff:3.500A) Processing helix chain 'l' and resid 478 through 488 Processing helix chain 'm' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN m 15 " --> pdb=" O SER m 11 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 99 Processing helix chain 'm' and resid 108 through 126 Processing helix chain 'm' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL m 390 " --> pdb=" O VAL m 387 " (cutoff:3.500A) Processing helix chain 'm' and resid 394 through 449 removed outlier: 3.552A pdb=" N ASN m 400 " --> pdb=" O ASP m 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN m 407 " --> pdb=" O ALA m 403 " (cutoff:3.500A) Processing helix chain 'm' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA m 457 " --> pdb=" O ALA m 453 " (cutoff:3.500A) Processing helix chain 'm' and resid 478 through 488 Processing helix chain 'n' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) Processing helix chain 'n' and resid 44 through 99 Processing helix chain 'n' and resid 108 through 126 Processing helix chain 'n' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL n 390 " --> pdb=" O VAL n 387 " (cutoff:3.500A) Processing helix chain 'n' and resid 394 through 449 removed outlier: 3.553A pdb=" N ASN n 400 " --> pdb=" O ASP n 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN n 407 " --> pdb=" O ALA n 403 " (cutoff:3.500A) Processing helix chain 'n' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA n 457 " --> pdb=" O ALA n 453 " (cutoff:3.500A) Processing helix chain 'n' and resid 478 through 488 Processing helix chain 'o' and resid 11 through 35 removed outlier: 3.935A pdb=" N GLN o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 44 through 99 Processing helix chain 'o' and resid 108 through 126 Processing helix chain 'o' and resid 386 through 390 removed outlier: 3.669A pdb=" N VAL o 390 " --> pdb=" O VAL o 387 " (cutoff:3.500A) Processing helix chain 'o' and resid 394 through 449 removed outlier: 3.553A pdb=" N ASN o 400 " --> pdb=" O ASP o 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN o 407 " --> pdb=" O ALA o 403 " (cutoff:3.500A) Processing helix chain 'o' and resid 451 through 477 removed outlier: 4.660A pdb=" N ALA o 457 " --> pdb=" O ALA o 453 " (cutoff:3.500A) Processing helix chain 'o' and resid 478 through 488 Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA2, first strand: chain 'B' and resid 146 through 148 Processing sheet with id=AA3, first strand: chain 'C' and resid 146 through 148 Processing sheet with id=AA4, first strand: chain 'D' and resid 146 through 148 Processing sheet with id=AA5, first strand: chain 'E' and resid 146 through 148 Processing sheet with id=AA6, first strand: chain 'F' and resid 146 through 148 Processing sheet with id=AA7, first strand: chain 'G' and resid 146 through 148 Processing sheet with id=AA8, first strand: chain 'H' and resid 146 through 148 Processing sheet with id=AA9, first strand: chain 'I' and resid 146 through 148 Processing sheet with id=AB1, first strand: chain 'J' and resid 146 through 148 Processing sheet with id=AB2, first strand: chain 'K' and resid 146 through 148 Processing sheet with id=AB3, first strand: chain 'L' and resid 146 through 148 Processing sheet with id=AB4, first strand: chain 'M' and resid 146 through 148 Processing sheet with id=AB5, first strand: chain 'N' and resid 146 through 148 Processing sheet with id=AB6, first strand: chain 'O' and resid 146 through 148 Processing sheet with id=AB7, first strand: chain 'P' and resid 146 through 148 Processing sheet with id=AB8, first strand: chain 'Q' and resid 146 through 148 Processing sheet with id=AB9, first strand: chain 'R' and resid 146 through 148 Processing sheet with id=AC1, first strand: chain 'S' and resid 146 through 148 Processing sheet with id=AC2, first strand: chain 'T' and resid 146 through 148 Processing sheet with id=AC3, first strand: chain 'U' and resid 146 through 148 Processing sheet with id=AC4, first strand: chain 'V' and resid 146 through 148 Processing sheet with id=AC5, first strand: chain 'W' and resid 146 through 148 Processing sheet with id=AC6, first strand: chain 'X' and resid 146 through 148 Processing sheet with id=AC7, first strand: chain 'Y' and resid 146 through 148 Processing sheet with id=AC8, first strand: chain 'Z' and resid 146 through 148 Processing sheet with id=AC9, first strand: chain 'a' and resid 146 through 148 Processing sheet with id=AD1, first strand: chain 'b' and resid 146 through 148 Processing sheet with id=AD2, first strand: chain 'c' and resid 146 through 148 Processing sheet with id=AD3, first strand: chain 'd' and resid 146 through 148 Processing sheet with id=AD4, first strand: chain 'e' and resid 146 through 148 Processing sheet with id=AD5, first strand: chain 'f' and resid 146 through 148 Processing sheet with id=AD6, first strand: chain 'g' and resid 146 through 148 Processing sheet with id=AD7, first strand: chain 'h' and resid 146 through 148 Processing sheet with id=AD8, first strand: chain 'i' and resid 146 through 148 Processing sheet with id=AD9, first strand: chain 'j' and resid 146 through 148 Processing sheet with id=AE1, first strand: chain 'k' and resid 146 through 148 Processing sheet with id=AE2, first strand: chain 'l' and resid 146 through 148 Processing sheet with id=AE3, first strand: chain 'm' and resid 146 through 148 Processing sheet with id=AE4, first strand: chain 'n' and resid 146 through 148 Processing sheet with id=AE5, first strand: chain 'o' and resid 146 through 148 6929 hydrogen bonds defined for protein. 20664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 53.93 Time building geometry restraints manager: 105.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.99: 80524 0.99 - 1.14: 0 1.14 - 1.30: 15170 1.30 - 1.45: 21048 1.45 - 1.60: 45167 Bond restraints: 161909 Sorted by residual: bond pdb=" CD LYS d 42 " pdb=" CE LYS d 42 " ideal model delta sigma weight residual 1.520 1.384 0.136 3.00e-02 1.11e+03 2.05e+01 bond pdb=" CD LYS T 42 " pdb=" CE LYS T 42 " ideal model delta sigma weight residual 1.520 1.384 0.136 3.00e-02 1.11e+03 2.05e+01 bond pdb=" CD LYS e 42 " pdb=" CE LYS e 42 " ideal model delta sigma weight residual 1.520 1.384 0.136 3.00e-02 1.11e+03 2.05e+01 bond pdb=" CD LYS I 42 " pdb=" CE LYS I 42 " ideal model delta sigma weight residual 1.520 1.384 0.136 3.00e-02 1.11e+03 2.05e+01 bond pdb=" CD LYS F 42 " pdb=" CE LYS F 42 " ideal model delta sigma weight residual 1.520 1.384 0.136 3.00e-02 1.11e+03 2.05e+01 ... (remaining 161904 not shown) Histogram of bond angle deviations from ideal: 99.10 - 105.14: 1225 105.14 - 111.18: 174420 111.18 - 117.22: 41223 117.22 - 123.26: 61085 123.26 - 129.30: 12901 Bond angle restraints: 290854 Sorted by residual: angle pdb=" C ALA P 41 " pdb=" N LYS P 42 " pdb=" CA LYS P 42 " ideal model delta sigma weight residual 120.38 127.92 -7.54 1.46e+00 4.69e-01 2.67e+01 angle pdb=" C ALA k 41 " pdb=" N LYS k 42 " pdb=" CA LYS k 42 " ideal model delta sigma weight residual 120.38 127.91 -7.53 1.46e+00 4.69e-01 2.66e+01 angle pdb=" C ALA c 41 " pdb=" N LYS c 42 " pdb=" CA LYS c 42 " ideal model delta sigma weight residual 120.38 127.91 -7.53 1.46e+00 4.69e-01 2.66e+01 angle pdb=" C ALA H 41 " pdb=" N LYS H 42 " pdb=" CA LYS H 42 " ideal model delta sigma weight residual 120.38 127.91 -7.53 1.46e+00 4.69e-01 2.66e+01 angle pdb=" C ALA j 41 " pdb=" N LYS j 42 " pdb=" CA LYS j 42 " ideal model delta sigma weight residual 120.38 127.90 -7.52 1.46e+00 4.69e-01 2.66e+01 ... (remaining 290849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.22: 59317 11.22 - 22.45: 3741 22.45 - 33.67: 861 33.67 - 44.89: 861 44.89 - 56.12: 123 Dihedral angle restraints: 64903 sinusoidal: 31529 harmonic: 33374 Sorted by residual: dihedral pdb=" CA ASP f 108 " pdb=" C ASP f 108 " pdb=" N ARG f 109 " pdb=" CA ARG f 109 " ideal model delta harmonic sigma weight residual 180.00 145.34 34.66 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA ASP Z 108 " pdb=" C ASP Z 108 " pdb=" N ARG Z 109 " pdb=" CA ARG Z 109 " ideal model delta harmonic sigma weight residual 180.00 145.34 34.66 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA ASP k 108 " pdb=" C ASP k 108 " pdb=" N ARG k 109 " pdb=" CA ARG k 109 " ideal model delta harmonic sigma weight residual 180.00 145.35 34.65 0 5.00e+00 4.00e-02 4.80e+01 ... (remaining 64900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 8209 0.044 - 0.088: 4081 0.088 - 0.132: 1237 0.132 - 0.175: 126 0.175 - 0.219: 82 Chirality restraints: 13735 Sorted by residual: chirality pdb=" CB VAL E 390 " pdb=" CA VAL E 390 " pdb=" CG1 VAL E 390 " pdb=" CG2 VAL E 390 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL X 390 " pdb=" CA VAL X 390 " pdb=" CG1 VAL X 390 " pdb=" CG2 VAL X 390 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL O 390 " pdb=" CA VAL O 390 " pdb=" CG1 VAL O 390 " pdb=" CG2 VAL O 390 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 13732 not shown) Planarity restraints: 25912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 13 " 0.036 2.00e-02 2.50e+03 3.11e-02 1.45e+01 pdb=" CG ASN H 13 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN H 13 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN H 13 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN H 13 " 0.044 2.00e-02 2.50e+03 pdb="HD22 ASN H 13 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN e 13 " -0.036 2.00e-02 2.50e+03 3.11e-02 1.45e+01 pdb=" CG ASN e 13 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN e 13 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN e 13 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN e 13 " -0.044 2.00e-02 2.50e+03 pdb="HD22 ASN e 13 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN h 13 " -0.036 2.00e-02 2.50e+03 3.11e-02 1.45e+01 pdb=" CG ASN h 13 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN h 13 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN h 13 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN h 13 " -0.044 2.00e-02 2.50e+03 pdb="HD22 ASN h 13 " 0.029 2.00e-02 2.50e+03 ... (remaining 25909 not shown) Histogram of nonbonded interaction distances: 1.31 - 1.95: 2773 1.95 - 2.58: 186236 2.58 - 3.22: 509059 3.22 - 3.86: 601538 3.86 - 4.50: 921942 Nonbonded interactions: 2221548 Sorted by model distance: nonbonded pdb=" O ILE b 430 " pdb=" HG1 THR b 434 " model vdw 1.307 1.850 nonbonded pdb=" O ILE S 430 " pdb=" HG1 THR S 434 " model vdw 1.307 1.850 nonbonded pdb=" O ILE W 430 " pdb=" HG1 THR W 434 " model vdw 1.307 1.850 nonbonded pdb=" O ILE f 430 " pdb=" HG1 THR f 434 " model vdw 1.307 1.850 nonbonded pdb=" O ILE K 430 " pdb=" HG1 THR K 434 " model vdw 1.307 1.850 ... (remaining 2221543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 48667 2.51 5 N 15211 2.21 5 O 17261 1.98 5 H 80524 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.710 Extract box with map and model: 18.380 Check model and map are aligned: 1.790 Convert atoms to be neutral: 1.000 Process input model: 357.440 Find NCS groups from input model: 6.470 Set up NCS constraints: 1.270 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 391.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.137 81385 Z= 0.851 Angle : 1.247 12.799 110454 Z= 0.738 Chirality : 0.055 0.219 13735 Planarity : 0.008 0.042 15006 Dihedral : 10.128 49.329 29438 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.07), residues: 10865 helix: -1.57 (0.05), residues: 7872 sheet: -3.90 (0.18), residues: 410 loop : -2.48 (0.11), residues: 2583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5071 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5071 time to evaluate : 8.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5071 average time/residue: 1.8566 time to fit residues: 15467.7536 Evaluate side-chains 2672 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2672 time to evaluate : 8.289 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.1640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 900 optimal weight: 20.0000 chunk 807 optimal weight: 9.9990 chunk 448 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 545 optimal weight: 5.9990 chunk 431 optimal weight: 9.9990 chunk 835 optimal weight: 1.9990 chunk 323 optimal weight: 9.9990 chunk 508 optimal weight: 3.9990 chunk 621 optimal weight: 7.9990 chunk 968 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 466 GLN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN ** B 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN B 466 GLN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** C 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 GLN ** D 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN E 467 GLN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 ASN F 466 GLN ** F 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN G 466 GLN ** G 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN ** H 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 466 GLN H 467 GLN ** H 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 466 GLN I 467 GLN ** I 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 428 ASN ** J 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 466 GLN ** J 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 428 ASN K 432 ASN K 439 ASN K 466 GLN ** K 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 ASN L 52 ASN ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 466 GLN L 481 GLN ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 439 ASN M 466 GLN M 467 GLN ** M 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 466 GLN ** N 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 23 ASN ** O 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN O 148 GLN ** O 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 466 GLN ** O 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 ASN P 466 GLN ** P 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 GLN ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 439 ASN Q 463 GLN Q 466 GLN ** Q 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN R 428 ASN R 439 ASN R 466 GLN R 467 GLN ** R 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 GLN ** S 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 466 GLN ** S 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 120 GLN ** T 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 439 ASN T 466 GLN ** T 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 148 GLN ** U 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 423 GLN U 424 ASN U 432 ASN ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 463 GLN U 466 GLN ** U 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 ASN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 466 GLN ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 ASN W 148 GLN ** W 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 423 GLN W 428 ASN ** W 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 466 GLN ** W 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** X 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 432 ASN X 466 GLN X 481 GLN ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 148 GLN ** Y 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 423 GLN ** Y 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 466 GLN ** Y 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 120 GLN ** Z 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 428 ASN ** Z 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 466 GLN ** Z 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 23 ASN a 76 GLN a 423 GLN ** a 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 466 GLN ** a 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 GLN ** b 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 424 ASN b 439 ASN b 466 GLN ** c 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 423 GLN ** c 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 466 GLN c 467 GLN c 481 GLN ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 466 GLN d 481 GLN ** e 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 17 ASN e 23 ASN ** e 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 423 GLN e 424 ASN e 428 ASN e 466 GLN ** e 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 466 GLN f 467 GLN f 481 GLN ** g 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 GLN ** g 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 423 GLN ** g 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 466 GLN ** g 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 463 GLN h 466 GLN h 481 GLN ** i 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 23 ASN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 423 GLN i 428 ASN ** i 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 466 GLN ** i 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 466 GLN j 481 GLN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 57 GLN k 148 GLN ** k 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 432 ASN k 439 ASN k 466 GLN k 481 GLN ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 466 GLN l 481 GLN ** m 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 148 GLN ** m 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 423 GLN m 466 GLN ** m 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 120 GLN ** n 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 466 GLN n 481 GLN ** o 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 423 GLN ** o 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 439 ASN o 466 GLN o 481 GLN Total number of N/Q/H flips: 135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 81385 Z= 0.277 Angle : 0.689 8.000 110454 Z= 0.408 Chirality : 0.039 0.162 13735 Planarity : 0.007 0.091 15006 Dihedral : 6.819 29.329 11685 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.08), residues: 10865 helix: 0.55 (0.06), residues: 8077 sheet: -3.21 (0.20), residues: 410 loop : -2.50 (0.12), residues: 2378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3393 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 3383 time to evaluate : 9.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 3393 average time/residue: 1.7676 time to fit residues: 9954.3386 Evaluate side-chains 2553 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2551 time to evaluate : 9.320 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.7366 time to fit residues: 17.4061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 537 optimal weight: 0.9990 chunk 300 optimal weight: 20.0000 chunk 805 optimal weight: 3.9990 chunk 659 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 969 optimal weight: 6.9990 chunk 1047 optimal weight: 10.0000 chunk 863 optimal weight: 10.0000 chunk 961 optimal weight: 9.9990 chunk 330 optimal weight: 8.9990 chunk 778 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 428 ASN ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 463 GLN H 477 ASN ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN ** I 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 463 GLN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 428 ASN ** J 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 463 GLN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 GLN ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 435 ASN ** L 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 463 GLN M 477 ASN N 83 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 463 GLN N 477 ASN ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 23 ASN ** O 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 463 GLN ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 399 GLN ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 428 ASN ** Q 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 477 ASN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 428 ASN ** R 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 463 GLN ** S 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 463 GLN ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 463 GLN ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 432 ASN ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 477 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 432 ASN V 463 GLN W 69 ASN ** W 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 463 GLN ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 399 GLN X 400 ASN X 432 ASN X 477 ASN ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 432 ASN ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 428 ASN Z 432 ASN ** a 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 23 ASN a 69 ASN ** a 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 432 ASN ** c 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 423 GLN ** c 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 463 GLN c 477 ASN ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 148 GLN ** d 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 428 ASN ** d 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 463 GLN ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 428 ASN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 83 GLN ** f 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 477 ASN ** h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 23 ASN ** i 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 83 GLN ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 148 GLN ** k 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 423 GLN ** k 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 83 GLN ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 477 ASN ** n 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 399 GLN ** n 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 428 ASN ** o 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 477 ASN o 481 GLN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.6177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 81385 Z= 0.253 Angle : 0.630 8.832 110454 Z= 0.369 Chirality : 0.037 0.160 13735 Planarity : 0.005 0.103 15006 Dihedral : 6.328 28.290 11685 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.54 % Favored : 92.43 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.08), residues: 10865 helix: 1.26 (0.06), residues: 8077 sheet: -2.97 (0.20), residues: 410 loop : -2.56 (0.12), residues: 2378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3174 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 3172 time to evaluate : 8.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 3174 average time/residue: 1.7700 time to fit residues: 9359.9101 Evaluate side-chains 2502 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2502 time to evaluate : 8.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.4698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 958 optimal weight: 8.9990 chunk 729 optimal weight: 20.0000 chunk 503 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 462 optimal weight: 20.0000 chunk 651 optimal weight: 20.0000 chunk 973 optimal weight: 10.0000 chunk 1030 optimal weight: 9.9990 chunk 508 optimal weight: 20.0000 chunk 922 optimal weight: 8.9990 chunk 277 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN B 428 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 GLN E 400 ASN E 428 ASN ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN E 481 GLN ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 ASN G 477 ASN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 477 ASN ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 400 ASN ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 428 ASN ** J 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 399 GLN K 400 ASN ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 463 GLN ** L 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 477 ASN ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 477 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 439 ASN N 477 ASN ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 83 GLN ** O 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 GLN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 477 ASN ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 428 ASN ** Q 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 477 ASN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN R 428 ASN ** R 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 400 ASN ** S 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 477 ASN ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 148 GLN ** U 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 477 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 428 ASN V 432 ASN V 442 ASN V 477 ASN W 148 GLN ** W 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 428 ASN ** W 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 432 ASN X 477 ASN ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 399 GLN ** Z 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 477 ASN ** a 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 463 GLN ** b 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 84 GLN ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 GLN b 400 ASN ** b 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 477 ASN ** c 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 423 GLN c 428 ASN ** c 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 477 ASN c 481 GLN ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 98 GLN ** f 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 GLN ** g 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 423 GLN ** g 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 477 ASN ** h 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 481 GLN ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 428 ASN ** k 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 477 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 423 GLN ** m 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 477 ASN n 62 ASN ** n 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 400 ASN n 481 GLN ** o 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 423 GLN ** o 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 439 ASN o 477 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 81385 Z= 0.285 Angle : 0.642 10.006 110454 Z= 0.375 Chirality : 0.037 0.159 13735 Planarity : 0.005 0.105 15006 Dihedral : 6.201 28.487 11685 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.08), residues: 10865 helix: 1.61 (0.06), residues: 7954 sheet: -2.52 (0.21), residues: 410 loop : -2.43 (0.11), residues: 2501 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3084 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 3081 time to evaluate : 9.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3083 average time/residue: 1.7457 time to fit residues: 8947.3821 Evaluate side-chains 2470 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2469 time to evaluate : 8.428 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.1943 time to fit residues: 12.5445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 858 optimal weight: 10.0000 chunk 584 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 767 optimal weight: 9.9990 chunk 425 optimal weight: 20.0000 chunk 879 optimal weight: 10.0000 chunk 712 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 526 optimal weight: 20.0000 chunk 924 optimal weight: 7.9990 chunk 260 optimal weight: 1.9990 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN E 428 ASN E 477 ASN F 57 GLN ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 ASN G 477 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN H 400 ASN ** H 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 477 ASN ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 428 ASN ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 428 ASN ** J 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 435 ASN L 477 ASN ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 400 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 477 ASN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 57 GLN ** O 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 400 ASN ** O 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 477 ASN ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 400 ASN ** Q 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 477 ASN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 428 ASN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 120 GLN T 399 GLN T 477 ASN ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 400 ASN ** U 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 477 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 400 ASN ** V 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 442 ASN V 477 ASN W 400 ASN ** W 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 477 ASN ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 17 ASN Y 400 ASN ** Y 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 400 ASN ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 463 GLN Z 477 ASN ** a 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 399 GLN b 477 ASN ** c 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 477 ASN d 62 ASN ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 400 ASN ** d 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 GLN ** e 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 400 ASN ** g 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 477 ASN ** h 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 400 ASN h 481 GLN ** i 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 400 ASN ** i 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 400 ASN k 400 ASN k 428 ASN ** k 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 477 ASN l 400 ASN ** l 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 477 ASN ** n 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 120 GLN n 481 GLN ** o 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 477 ASN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.7460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 81385 Z= 0.270 Angle : 0.620 9.688 110454 Z= 0.362 Chirality : 0.037 0.176 13735 Planarity : 0.004 0.087 15006 Dihedral : 6.127 26.287 11685 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.08), residues: 10865 helix: 1.75 (0.06), residues: 7954 sheet: -2.29 (0.22), residues: 410 loop : -2.47 (0.12), residues: 2501 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3104 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 3102 time to evaluate : 8.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 3103 average time/residue: 1.6797 time to fit residues: 8651.5200 Evaluate side-chains 2480 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2480 time to evaluate : 8.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.2625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 346 optimal weight: 9.9990 chunk 927 optimal weight: 30.0000 chunk 203 optimal weight: 7.9990 chunk 604 optimal weight: 30.0000 chunk 254 optimal weight: 9.9990 chunk 1031 optimal weight: 5.9990 chunk 856 optimal weight: 9.9990 chunk 477 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 341 optimal weight: 10.0000 chunk 541 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 57 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN E 481 GLN ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 442 ASN H 477 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 477 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 477 ASN ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 400 ASN ** N 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 428 ASN ** Q 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 477 ASN ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 477 ASN ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 120 GLN ** T 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 477 ASN ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 477 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 428 ASN ** V 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 442 ASN ** W 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 467 GLN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 477 ASN Y 148 GLN ** Y 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 120 GLN ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 415 GLN ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 GLN b 162 GLN ** b 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 477 ASN c 428 ASN ** c 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 477 ASN d 69 ASN ** d 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 400 ASN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 400 ASN f 467 GLN g 162 GLN ** g 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 477 ASN ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 162 GLN i 162 GLN i 423 GLN ** i 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 162 GLN ** j 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 481 GLN k 162 GLN ** k 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 477 ASN m 120 GLN m 400 ASN ** m 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 477 ASN ** n 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 120 GLN ** n 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 477 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.7942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 81385 Z= 0.283 Angle : 0.630 6.395 110454 Z= 0.369 Chirality : 0.037 0.161 13735 Planarity : 0.005 0.071 15006 Dihedral : 6.106 26.105 11685 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.08), residues: 10865 helix: 1.73 (0.06), residues: 7954 sheet: -2.22 (0.22), residues: 410 loop : -2.58 (0.11), residues: 2501 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3061 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 3059 time to evaluate : 8.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 3061 average time/residue: 1.6618 time to fit residues: 8462.1106 Evaluate side-chains 2409 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2409 time to evaluate : 8.330 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.3806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 994 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 587 optimal weight: 20.0000 chunk 753 optimal weight: 5.9990 chunk 583 optimal weight: 20.0000 chunk 868 optimal weight: 30.0000 chunk 575 optimal weight: 7.9990 chunk 1027 optimal weight: 7.9990 chunk 642 optimal weight: 6.9990 chunk 626 optimal weight: 7.9990 chunk 474 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 162 GLN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN A 477 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN E 481 GLN ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 ASN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 428 ASN ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 477 ASN ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 428 ASN ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN I 481 GLN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 428 ASN ** J 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 477 ASN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 477 ASN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 477 ASN ** P 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 477 ASN ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 477 ASN ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 57 GLN ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 477 ASN ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 477 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 442 ASN ** W 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 477 ASN ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 120 GLN ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 477 ASN ** c 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 477 ASN d 120 GLN d 148 GLN ** d 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 477 ASN ** h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 57 GLN ** i 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 162 GLN ** j 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 481 GLN k 428 ASN ** k 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 477 ASN ** m 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 477 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.8268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 81385 Z= 0.256 Angle : 0.602 6.603 110454 Z= 0.351 Chirality : 0.037 0.155 13735 Planarity : 0.004 0.077 15006 Dihedral : 6.031 26.957 11685 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.08), residues: 10865 helix: 1.86 (0.06), residues: 7954 sheet: -2.19 (0.22), residues: 410 loop : -2.48 (0.12), residues: 2501 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2990 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2988 time to evaluate : 8.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2990 average time/residue: 1.6468 time to fit residues: 8214.6866 Evaluate side-chains 2377 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2376 time to evaluate : 8.297 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.4972 time to fit residues: 12.8043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 635 optimal weight: 10.0000 chunk 410 optimal weight: 2.9990 chunk 613 optimal weight: 20.0000 chunk 309 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 199 optimal weight: 4.9990 chunk 653 optimal weight: 0.3980 chunk 699 optimal weight: 7.9990 chunk 507 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 807 optimal weight: 20.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 GLN ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 ASN ** G 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 477 ASN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN ** P 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 428 ASN ** Q 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 477 ASN ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 57 GLN ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 442 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 477 ASN ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 120 GLN ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 477 ASN ** c 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 428 ASN ** c 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 120 GLN d 148 GLN ** d 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 17 ASN ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 GLN g 428 ASN ** g 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 162 GLN ** j 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 477 ASN l 90 GLN ** m 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.8457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 81385 Z= 0.203 Angle : 0.575 5.433 110454 Z= 0.331 Chirality : 0.036 0.153 13735 Planarity : 0.004 0.079 15006 Dihedral : 5.863 26.628 11685 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.08), residues: 10865 helix: 2.00 (0.06), residues: 7954 sheet: -2.14 (0.23), residues: 410 loop : -2.27 (0.12), residues: 2501 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2992 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2992 time to evaluate : 8.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2992 average time/residue: 1.6445 time to fit residues: 8221.7920 Evaluate side-chains 2381 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2381 time to evaluate : 8.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.2199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 934 optimal weight: 8.9990 chunk 984 optimal weight: 20.0000 chunk 898 optimal weight: 9.9990 chunk 957 optimal weight: 9.9990 chunk 576 optimal weight: 9.9990 chunk 417 optimal weight: 6.9990 chunk 751 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 865 optimal weight: 6.9990 chunk 905 optimal weight: 9.9990 chunk 954 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN E 481 GLN ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 428 ASN ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 477 ASN ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 428 ASN I 481 GLN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 ASN ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 463 GLN ** N 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 477 ASN ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 481 GLN ** S 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 442 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 477 ASN ** Y 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 477 ASN ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 120 GLN ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 477 ASN ** c 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 477 ASN d 15 GLN ** d 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 415 GLN g 477 ASN ** h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 428 ASN k 477 ASN ** m 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.8649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 81385 Z= 0.253 Angle : 0.606 10.212 110454 Z= 0.352 Chirality : 0.037 0.179 13735 Planarity : 0.004 0.125 15006 Dihedral : 5.885 26.268 11685 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.08), residues: 10865 helix: 1.93 (0.06), residues: 7954 sheet: -2.18 (0.23), residues: 410 loop : -2.33 (0.12), residues: 2501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2975 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2968 time to evaluate : 8.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 2975 average time/residue: 1.6897 time to fit residues: 8429.7319 Evaluate side-chains 2358 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2357 time to evaluate : 9.251 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.3359 time to fit residues: 13.8870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 628 optimal weight: 10.0000 chunk 1012 optimal weight: 2.9990 chunk 617 optimal weight: 20.0000 chunk 480 optimal weight: 20.0000 chunk 703 optimal weight: 20.0000 chunk 1062 optimal weight: 10.0000 chunk 977 optimal weight: 9.9990 chunk 845 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 653 optimal weight: 1.9990 chunk 518 optimal weight: 10.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 ASN ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 477 ASN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 ASN I 477 ASN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 428 ASN ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 477 ASN ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 428 ASN ** Q 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 481 GLN ** S 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 477 ASN ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 442 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 GLN Y 477 ASN ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 120 GLN ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 84 GLN ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 428 ASN ** c 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 432 ASN g 415 GLN ** h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 477 ASN ** m 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.8836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 81385 Z= 0.233 Angle : 0.590 8.427 110454 Z= 0.341 Chirality : 0.036 0.180 13735 Planarity : 0.004 0.094 15006 Dihedral : 5.818 26.511 11685 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.08), residues: 10865 helix: 1.98 (0.06), residues: 7954 sheet: -2.22 (0.23), residues: 410 loop : -2.26 (0.12), residues: 2501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21730 Ramachandran restraints generated. 10865 Oldfield, 0 Emsley, 10865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2988 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2987 time to evaluate : 8.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 2988 average time/residue: 1.6357 time to fit residues: 8198.1485 Evaluate side-chains 2343 residues out of total 8651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2343 time to evaluate : 8.374 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.2323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 671 optimal weight: 5.9990 chunk 900 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 779 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 847 optimal weight: 4.9990 chunk 354 optimal weight: 20.0000 chunk 869 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 481 GLN ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 428 ASN ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 477 ASN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 428 ASN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 477 ASN Q 17 ASN ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 481 GLN ** S 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 23 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 477 ASN ** Y 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 120 GLN ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 477 ASN ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 148 GLN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 415 GLN ** g 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 477 ASN ** h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 57 GLN ** i 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 477 ASN ** j 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 428 ASN ** m 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.129151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.120217 restraints weight = 519563.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.123753 restraints weight = 242515.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.125736 restraints weight = 123980.740| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.8984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 81385 Z= 0.222 Angle : 0.584 8.518 110454 Z= 0.337 Chirality : 0.036 0.175 13735 Planarity : 0.004 0.115 15006 Dihedral : 5.764 26.033 11685 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.08), residues: 10865 helix: 2.05 (0.06), residues: 7954 sheet: -2.24 (0.23), residues: 410 loop : -2.22 (0.12), residues: 2501 =============================================================================== Job complete usr+sys time: 101149.68 seconds wall clock time: 1715 minutes 49.39 seconds (102949.39 seconds total)