Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 15:18:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq7_6675/04_2023/5wq7_6675_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq7_6675/04_2023/5wq7_6675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq7_6675/04_2023/5wq7_6675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq7_6675/04_2023/5wq7_6675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq7_6675/04_2023/5wq7_6675_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq7_6675/04_2023/5wq7_6675_neut.pdb" } resolution = 3.04 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= 0.000 sd= 0.005 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 34185 2.51 5 N 9420 2.21 5 O 10800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 551": "NH1" <-> "NH2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "C ARG 551": "NH1" <-> "NH2" Residue "D ARG 551": "NH1" <-> "NH2" Residue "E ARG 551": "NH1" <-> "NH2" Residue "F ARG 551": "NH1" <-> "NH2" Residue "G ARG 551": "NH1" <-> "NH2" Residue "H ARG 551": "NH1" <-> "NH2" Residue "I ARG 551": "NH1" <-> "NH2" Residue "J ARG 551": "NH1" <-> "NH2" Residue "K ARG 551": "NH1" <-> "NH2" Residue "L ARG 551": "NH1" <-> "NH2" Residue "M ARG 551": "NH1" <-> "NH2" Residue "N ARG 551": "NH1" <-> "NH2" Residue "O ARG 551": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 54480 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "B" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "C" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "D" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "E" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "F" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "G" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "H" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "I" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "J" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "K" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "L" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "M" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "N" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Chain: "O" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Time building chain proxies: 19.84, per 1000 atoms: 0.36 Number of scatterers: 54480 At special positions: 0 Unit cell: (162.36, 161.04, 192.72, 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) S 75 16.00 O 10800 8.00 N 9420 7.00 C 34185 6.00 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: 16.16 Conformation dependent library (CDL) restraints added in 6.1 seconds 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13230 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 48 sheets defined 31.6% alpha, 46.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP A 116 " --> pdb=" O PRO A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 147 through 164 Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP B 116 " --> pdb=" O PRO B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 147 through 164 Processing helix chain 'B' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 235 Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 265 " --> pdb=" O VAL B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 Processing helix chain 'B' and resid 545 through 550 Processing helix chain 'B' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 584 " --> pdb=" O LEU B 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP C 116 " --> pdb=" O PRO C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 113 through 116' Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 147 through 164 Processing helix chain 'C' and resid 178 through 188 removed outlier: 3.737A pdb=" N LEU C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 235 Processing helix chain 'C' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 265 " --> pdb=" O VAL C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 377 Processing helix chain 'C' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 545 through 550 Processing helix chain 'C' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER C 579 " --> pdb=" O ASP C 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 584 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 116 removed outlier: 3.748A pdb=" N ASP D 116 " --> pdb=" O PRO D 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 113 through 116' Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 147 through 164 Processing helix chain 'D' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 235 Processing helix chain 'D' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU D 260 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 261 " --> pdb=" O ASN D 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 265 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 377 Processing helix chain 'D' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 543 Processing helix chain 'D' and resid 545 through 550 Processing helix chain 'D' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER D 579 " --> pdb=" O ASP D 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS D 584 " --> pdb=" O LEU D 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP E 116 " --> pdb=" O PRO E 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 113 through 116' Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 147 through 164 Processing helix chain 'E' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN E 188 " --> pdb=" O GLU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 235 Processing helix chain 'E' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 261 " --> pdb=" O ASN E 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 265 " --> pdb=" O VAL E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 377 Processing helix chain 'E' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA E 391 " --> pdb=" O ASP E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 543 Processing helix chain 'E' and resid 545 through 550 Processing helix chain 'E' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR E 577 " --> pdb=" O ASP E 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER E 579 " --> pdb=" O ASP E 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS E 584 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP F 116 " --> pdb=" O PRO F 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 113 through 116' Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'F' and resid 147 through 164 Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU F 182 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 235 Processing helix chain 'F' and resid 254 through 267 removed outlier: 3.654A pdb=" N GLU F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 261 " --> pdb=" O ASN F 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY F 264 " --> pdb=" O GLU F 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL F 265 " --> pdb=" O VAL F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 377 Processing helix chain 'F' and resid 385 through 391 removed outlier: 3.551A pdb=" N ALA F 391 " --> pdb=" O ASP F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 543 Processing helix chain 'F' and resid 545 through 550 Processing helix chain 'F' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR F 577 " --> pdb=" O ASP F 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER F 579 " --> pdb=" O ASP F 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS F 584 " --> pdb=" O LEU F 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP G 116 " --> pdb=" O PRO G 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 113 through 116' Processing helix chain 'G' and resid 117 through 126 Processing helix chain 'G' and resid 147 through 164 Processing helix chain 'G' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU G 182 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 235 Processing helix chain 'G' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU G 260 " --> pdb=" O THR G 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL G 261 " --> pdb=" O ASN G 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL G 265 " --> pdb=" O VAL G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR G 313 " --> pdb=" O GLU G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 377 Processing helix chain 'G' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA G 391 " --> pdb=" O ASP G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 543 Processing helix chain 'G' and resid 545 through 550 Processing helix chain 'G' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR G 577 " --> pdb=" O ASP G 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER G 579 " --> pdb=" O ASP G 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS G 584 " --> pdb=" O LEU G 580 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP H 116 " --> pdb=" O PRO H 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 113 through 116' Processing helix chain 'H' and resid 117 through 126 Processing helix chain 'H' and resid 147 through 164 Processing helix chain 'H' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU H 182 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN H 188 " --> pdb=" O GLU H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 235 Processing helix chain 'H' and resid 254 through 267 removed outlier: 3.654A pdb=" N GLU H 260 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL H 261 " --> pdb=" O ASN H 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY H 264 " --> pdb=" O GLU H 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL H 265 " --> pdb=" O VAL H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR H 313 " --> pdb=" O GLU H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 377 Processing helix chain 'H' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA H 391 " --> pdb=" O ASP H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 543 Processing helix chain 'H' and resid 545 through 550 Processing helix chain 'H' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR H 577 " --> pdb=" O ASP H 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER H 579 " --> pdb=" O ASP H 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS H 584 " --> pdb=" O LEU H 580 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP I 116 " --> pdb=" O PRO I 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 113 through 116' Processing helix chain 'I' and resid 117 through 126 Processing helix chain 'I' and resid 147 through 164 Processing helix chain 'I' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU I 182 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN I 188 " --> pdb=" O GLU I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 235 Processing helix chain 'I' and resid 254 through 267 removed outlier: 3.654A pdb=" N GLU I 260 " --> pdb=" O THR I 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL I 261 " --> pdb=" O ASN I 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY I 264 " --> pdb=" O GLU I 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL I 265 " --> pdb=" O VAL I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR I 313 " --> pdb=" O GLU I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 377 Processing helix chain 'I' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA I 391 " --> pdb=" O ASP I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 539 through 543 Processing helix chain 'I' and resid 545 through 550 Processing helix chain 'I' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR I 577 " --> pdb=" O ASP I 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER I 579 " --> pdb=" O ASP I 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS I 584 " --> pdb=" O LEU I 580 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP J 116 " --> pdb=" O PRO J 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 113 through 116' Processing helix chain 'J' and resid 117 through 126 Processing helix chain 'J' and resid 147 through 164 Processing helix chain 'J' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU J 182 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 235 Processing helix chain 'J' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU J 260 " --> pdb=" O THR J 256 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL J 261 " --> pdb=" O ASN J 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY J 264 " --> pdb=" O GLU J 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL J 265 " --> pdb=" O VAL J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR J 313 " --> pdb=" O GLU J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 377 Processing helix chain 'J' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA J 391 " --> pdb=" O ASP J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 539 through 543 Processing helix chain 'J' and resid 545 through 550 Processing helix chain 'J' and resid 573 through 599 removed outlier: 3.572A pdb=" N TYR J 577 " --> pdb=" O ASP J 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER J 579 " --> pdb=" O ASP J 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS J 584 " --> pdb=" O LEU J 580 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP K 116 " --> pdb=" O PRO K 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 113 through 116' Processing helix chain 'K' and resid 117 through 126 Processing helix chain 'K' and resid 147 through 164 Processing helix chain 'K' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU K 182 " --> pdb=" O SER K 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN K 188 " --> pdb=" O GLU K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 235 Processing helix chain 'K' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU K 260 " --> pdb=" O THR K 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL K 261 " --> pdb=" O ASN K 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY K 264 " --> pdb=" O GLU K 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL K 265 " --> pdb=" O VAL K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR K 313 " --> pdb=" O GLU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 377 Processing helix chain 'K' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA K 391 " --> pdb=" O ASP K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 539 through 543 Processing helix chain 'K' and resid 545 through 550 Processing helix chain 'K' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR K 577 " --> pdb=" O ASP K 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER K 579 " --> pdb=" O ASP K 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS K 584 " --> pdb=" O LEU K 580 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 116 removed outlier: 3.748A pdb=" N ASP L 116 " --> pdb=" O PRO L 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 113 through 116' Processing helix chain 'L' and resid 117 through 126 Processing helix chain 'L' and resid 147 through 164 Processing helix chain 'L' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU L 182 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN L 188 " --> pdb=" O GLU L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 235 Processing helix chain 'L' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU L 260 " --> pdb=" O THR L 256 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL L 261 " --> pdb=" O ASN L 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL L 265 " --> pdb=" O VAL L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR L 313 " --> pdb=" O GLU L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 377 Processing helix chain 'L' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA L 391 " --> pdb=" O ASP L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 539 through 543 Processing helix chain 'L' and resid 545 through 550 Processing helix chain 'L' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR L 577 " --> pdb=" O ASP L 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 579 " --> pdb=" O ASP L 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS L 584 " --> pdb=" O LEU L 580 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP M 116 " --> pdb=" O PRO M 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 113 through 116' Processing helix chain 'M' and resid 117 through 126 Processing helix chain 'M' and resid 147 through 164 Processing helix chain 'M' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU M 182 " --> pdb=" O SER M 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN M 188 " --> pdb=" O GLU M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 235 Processing helix chain 'M' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU M 260 " --> pdb=" O THR M 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL M 261 " --> pdb=" O ASN M 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY M 264 " --> pdb=" O GLU M 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL M 265 " --> pdb=" O VAL M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR M 313 " --> pdb=" O GLU M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 362 through 377 Processing helix chain 'M' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA M 391 " --> pdb=" O ASP M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 539 through 543 Processing helix chain 'M' and resid 545 through 550 Processing helix chain 'M' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR M 577 " --> pdb=" O ASP M 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER M 579 " --> pdb=" O ASP M 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS M 584 " --> pdb=" O LEU M 580 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 116 removed outlier: 3.748A pdb=" N ASP N 116 " --> pdb=" O PRO N 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 113 through 116' Processing helix chain 'N' and resid 117 through 126 Processing helix chain 'N' and resid 147 through 164 Processing helix chain 'N' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU N 182 " --> pdb=" O SER N 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN N 188 " --> pdb=" O GLU N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 235 Processing helix chain 'N' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU N 260 " --> pdb=" O THR N 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL N 261 " --> pdb=" O ASN N 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY N 264 " --> pdb=" O GLU N 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL N 265 " --> pdb=" O VAL N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR N 313 " --> pdb=" O GLU N 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 362 through 377 Processing helix chain 'N' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA N 391 " --> pdb=" O ASP N 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 539 through 543 Processing helix chain 'N' and resid 545 through 550 Processing helix chain 'N' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR N 577 " --> pdb=" O ASP N 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER N 579 " --> pdb=" O ASP N 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS N 584 " --> pdb=" O LEU N 580 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP O 116 " --> pdb=" O PRO O 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 113 through 116' Processing helix chain 'O' and resid 117 through 126 Processing helix chain 'O' and resid 147 through 164 Processing helix chain 'O' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU O 182 " --> pdb=" O SER O 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN O 188 " --> pdb=" O GLU O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 235 Processing helix chain 'O' and resid 254 through 267 removed outlier: 3.654A pdb=" N GLU O 260 " --> pdb=" O THR O 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL O 261 " --> pdb=" O ASN O 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY O 264 " --> pdb=" O GLU O 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL O 265 " --> pdb=" O VAL O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR O 313 " --> pdb=" O GLU O 309 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 377 Processing helix chain 'O' and resid 385 through 391 removed outlier: 3.551A pdb=" N ALA O 391 " --> pdb=" O ASP O 387 " (cutoff:3.500A) Processing helix chain 'O' and resid 539 through 543 Processing helix chain 'O' and resid 545 through 550 Processing helix chain 'O' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR O 577 " --> pdb=" O ASP O 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER O 579 " --> pdb=" O ASP O 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS O 584 " --> pdb=" O LEU O 580 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 108 Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 173 Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 249 Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 348 removed outlier: 3.571A pdb=" N ARG A 557 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 566 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL A 521 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 16.518A pdb=" N VAL A 520 " --> pdb=" O LEU O 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU O 428 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 522 " --> pdb=" O VAL O 426 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP O 346 " --> pdb=" O GLN O 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP N 346 " --> pdb=" O GLN N 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP M 346 " --> pdb=" O GLN M 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP L 346 " --> pdb=" O GLN L 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP K 346 " --> pdb=" O GLN K 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP J 346 " --> pdb=" O GLN J 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP I 346 " --> pdb=" O GLN I 354 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP H 346 " --> pdb=" O GLN H 354 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP G 346 " --> pdb=" O GLN G 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP F 346 " --> pdb=" O GLN F 354 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 346 " --> pdb=" O GLN E 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP D 346 " --> pdb=" O GLN D 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 346 " --> pdb=" O GLN C 354 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP B 346 " --> pdb=" O GLN B 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 348 removed outlier: 3.522A pdb=" N TRP A 346 " --> pdb=" O GLN A 354 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG O 557 " --> pdb=" O ASN O 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE O 566 " --> pdb=" O VAL O 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL O 521 " --> pdb=" O ILE O 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL O 520 " --> pdb=" O LEU N 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU N 428 " --> pdb=" O VAL O 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU O 522 " --> pdb=" O VAL N 426 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG N 557 " --> pdb=" O ASN N 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE N 566 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL N 521 " --> pdb=" O ILE N 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL N 520 " --> pdb=" O LEU M 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU M 428 " --> pdb=" O VAL N 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU N 522 " --> pdb=" O VAL M 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG M 557 " --> pdb=" O ASN M 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE M 566 " --> pdb=" O VAL M 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL M 521 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 16.518A pdb=" N VAL M 520 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU L 428 " --> pdb=" O VAL M 520 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU M 522 " --> pdb=" O VAL L 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG L 557 " --> pdb=" O ASN L 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE L 566 " --> pdb=" O VAL L 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL L 521 " --> pdb=" O ILE L 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL L 520 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU K 428 " --> pdb=" O VAL L 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU L 522 " --> pdb=" O VAL K 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG K 557 " --> pdb=" O ASN K 338 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE K 566 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL K 521 " --> pdb=" O ILE K 566 " (cutoff:3.500A) removed outlier: 16.516A pdb=" N VAL K 520 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU J 428 " --> pdb=" O VAL K 520 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU K 522 " --> pdb=" O VAL J 426 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG J 557 " --> pdb=" O ASN J 338 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE J 566 " --> pdb=" O VAL J 521 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VAL J 521 " --> pdb=" O ILE J 566 " (cutoff:3.500A) removed outlier: 16.518A pdb=" N VAL J 520 " --> pdb=" O LEU I 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU I 428 " --> pdb=" O VAL J 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU J 522 " --> pdb=" O VAL I 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG I 557 " --> pdb=" O ASN I 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE I 566 " --> pdb=" O VAL I 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL I 521 " --> pdb=" O ILE I 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL I 520 " --> pdb=" O LEU H 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU H 428 " --> pdb=" O VAL I 520 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU I 522 " --> pdb=" O VAL H 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG H 557 " --> pdb=" O ASN H 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE H 566 " --> pdb=" O VAL H 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL H 521 " --> pdb=" O ILE H 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL H 520 " --> pdb=" O LEU G 428 " (cutoff:3.500A) removed outlier: 12.659A pdb=" N LEU G 428 " --> pdb=" O VAL H 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU H 522 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG G 557 " --> pdb=" O ASN G 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE G 566 " --> pdb=" O VAL G 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL G 521 " --> pdb=" O ILE G 566 " (cutoff:3.500A) removed outlier: 16.516A pdb=" N VAL G 520 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU F 428 " --> pdb=" O VAL G 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU G 522 " --> pdb=" O VAL F 426 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG F 557 " --> pdb=" O ASN F 338 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE F 566 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL F 521 " --> pdb=" O ILE F 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL F 520 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU E 428 " --> pdb=" O VAL F 520 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU F 522 " --> pdb=" O VAL E 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG E 557 " --> pdb=" O ASN E 338 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE E 566 " --> pdb=" O VAL E 521 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL E 521 " --> pdb=" O ILE E 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL E 520 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU D 428 " --> pdb=" O VAL E 520 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU E 522 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 557 " --> pdb=" O ASN D 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE D 566 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL D 521 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 16.516A pdb=" N VAL D 520 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU C 428 " --> pdb=" O VAL D 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU D 522 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 557 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 566 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL C 521 " --> pdb=" O ILE C 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL C 520 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU B 428 " --> pdb=" O VAL C 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU C 522 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 557 " --> pdb=" O ASN B 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 566 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL B 521 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL B 520 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU A 428 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 522 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 433 through 443 removed outlier: 12.674A pdb=" N THR A 463 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL A 491 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR O 463 " --> pdb=" O VAL O 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL O 491 " --> pdb=" O THR O 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR N 463 " --> pdb=" O VAL N 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL N 491 " --> pdb=" O THR N 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR M 463 " --> pdb=" O VAL M 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL M 491 " --> pdb=" O THR M 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR L 463 " --> pdb=" O VAL L 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL L 491 " --> pdb=" O THR L 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR K 463 " --> pdb=" O VAL K 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL K 491 " --> pdb=" O THR K 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR J 463 " --> pdb=" O VAL J 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL J 491 " --> pdb=" O THR J 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR I 463 " --> pdb=" O VAL I 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL I 491 " --> pdb=" O THR I 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR H 463 " --> pdb=" O VAL H 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL H 491 " --> pdb=" O THR H 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR G 463 " --> pdb=" O VAL G 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL G 491 " --> pdb=" O THR G 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR F 463 " --> pdb=" O VAL F 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL F 491 " --> pdb=" O THR F 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR E 463 " --> pdb=" O VAL E 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL E 491 " --> pdb=" O THR E 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR D 463 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL D 491 " --> pdb=" O THR D 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR C 463 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL C 491 " --> pdb=" O THR C 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR B 463 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL B 491 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 108 Processing sheet with id=AA8, first strand: chain 'B' and resid 170 through 173 Processing sheet with id=AA9, first strand: chain 'B' and resid 245 through 249 Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 108 Processing sheet with id=AB2, first strand: chain 'C' and resid 170 through 173 Processing sheet with id=AB3, first strand: chain 'C' and resid 245 through 249 Processing sheet with id=AB4, first strand: chain 'D' and resid 103 through 108 Processing sheet with id=AB5, first strand: chain 'D' and resid 170 through 173 Processing sheet with id=AB6, first strand: chain 'D' and resid 245 through 249 Processing sheet with id=AB7, first strand: chain 'E' and resid 103 through 108 Processing sheet with id=AB8, first strand: chain 'E' and resid 170 through 173 Processing sheet with id=AB9, first strand: chain 'E' and resid 245 through 249 Processing sheet with id=AC1, first strand: chain 'F' and resid 103 through 108 Processing sheet with id=AC2, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AC3, first strand: chain 'F' and resid 245 through 249 Processing sheet with id=AC4, first strand: chain 'G' and resid 103 through 108 Processing sheet with id=AC5, first strand: chain 'G' and resid 170 through 173 Processing sheet with id=AC6, first strand: chain 'G' and resid 245 through 249 Processing sheet with id=AC7, first strand: chain 'H' and resid 103 through 108 Processing sheet with id=AC8, first strand: chain 'H' and resid 170 through 173 Processing sheet with id=AC9, first strand: chain 'H' and resid 245 through 249 Processing sheet with id=AD1, first strand: chain 'I' and resid 103 through 108 Processing sheet with id=AD2, first strand: chain 'I' and resid 170 through 173 Processing sheet with id=AD3, first strand: chain 'I' and resid 245 through 249 Processing sheet with id=AD4, first strand: chain 'J' and resid 103 through 108 Processing sheet with id=AD5, first strand: chain 'J' and resid 170 through 173 Processing sheet with id=AD6, first strand: chain 'J' and resid 245 through 249 Processing sheet with id=AD7, first strand: chain 'K' and resid 103 through 108 Processing sheet with id=AD8, first strand: chain 'K' and resid 170 through 173 Processing sheet with id=AD9, first strand: chain 'K' and resid 245 through 249 Processing sheet with id=AE1, first strand: chain 'L' and resid 103 through 108 Processing sheet with id=AE2, first strand: chain 'L' and resid 170 through 173 Processing sheet with id=AE3, first strand: chain 'L' and resid 245 through 249 Processing sheet with id=AE4, first strand: chain 'M' and resid 103 through 108 Processing sheet with id=AE5, first strand: chain 'M' and resid 170 through 173 Processing sheet with id=AE6, first strand: chain 'M' and resid 245 through 249 Processing sheet with id=AE7, first strand: chain 'N' and resid 103 through 108 Processing sheet with id=AE8, first strand: chain 'N' and resid 170 through 173 Processing sheet with id=AE9, first strand: chain 'N' and resid 245 through 249 Processing sheet with id=AF1, first strand: chain 'O' and resid 103 through 108 Processing sheet with id=AF2, first strand: chain 'O' and resid 170 through 173 Processing sheet with id=AF3, first strand: chain 'O' and resid 245 through 249 4005 hydrogen bonds defined for protein. 11160 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: 19.71 Time building geometry restraints manager: 17.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 9675 1.31 - 1.44: 12615 1.44 - 1.56: 32655 1.56 - 1.68: 0 1.68 - 1.80: 150 Bond restraints: 55095 Sorted by residual: bond pdb=" C GLN L 345 " pdb=" O GLN L 345 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.14e-02 7.69e+03 1.38e+01 bond pdb=" C GLN I 345 " pdb=" O GLN I 345 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.14e-02 7.69e+03 1.38e+01 bond pdb=" C GLN J 345 " pdb=" O GLN J 345 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.14e-02 7.69e+03 1.37e+01 bond pdb=" C GLN H 345 " pdb=" O GLN H 345 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.14e-02 7.69e+03 1.37e+01 bond pdb=" C GLN G 345 " pdb=" O GLN G 345 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.14e-02 7.69e+03 1.37e+01 ... (remaining 55090 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.56: 1215 106.56 - 113.43: 31927 113.43 - 120.29: 19204 120.29 - 127.16: 21994 127.16 - 134.03: 405 Bond angle restraints: 74745 Sorted by residual: angle pdb=" C SER H 266 " pdb=" CA SER H 266 " pdb=" CB SER H 266 " ideal model delta sigma weight residual 110.38 99.70 10.68 2.04e+00 2.40e-01 2.74e+01 angle pdb=" C SER L 266 " pdb=" CA SER L 266 " pdb=" CB SER L 266 " ideal model delta sigma weight residual 110.38 99.70 10.68 2.04e+00 2.40e-01 2.74e+01 angle pdb=" C SER B 266 " pdb=" CA SER B 266 " pdb=" CB SER B 266 " ideal model delta sigma weight residual 110.38 99.73 10.65 2.04e+00 2.40e-01 2.73e+01 angle pdb=" C SER D 266 " pdb=" CA SER D 266 " pdb=" CB SER D 266 " ideal model delta sigma weight residual 110.38 99.73 10.65 2.04e+00 2.40e-01 2.72e+01 angle pdb=" C SER O 266 " pdb=" CA SER O 266 " pdb=" CB SER O 266 " ideal model delta sigma weight residual 110.38 99.74 10.64 2.04e+00 2.40e-01 2.72e+01 ... (remaining 74740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 31770 16.55 - 33.10: 1500 33.10 - 49.65: 375 49.65 - 66.20: 75 66.20 - 82.75: 60 Dihedral angle restraints: 33780 sinusoidal: 13365 harmonic: 20415 Sorted by residual: dihedral pdb=" CA THR E 166 " pdb=" C THR E 166 " pdb=" N GLU E 167 " pdb=" CA GLU E 167 " ideal model delta harmonic sigma weight residual 180.00 145.89 34.11 0 5.00e+00 4.00e-02 4.65e+01 dihedral pdb=" CA THR F 166 " pdb=" C THR F 166 " pdb=" N GLU F 167 " pdb=" CA GLU F 167 " ideal model delta harmonic sigma weight residual 180.00 145.89 34.11 0 5.00e+00 4.00e-02 4.65e+01 dihedral pdb=" CA THR J 166 " pdb=" C THR J 166 " pdb=" N GLU J 167 " pdb=" CA GLU J 167 " ideal model delta harmonic sigma weight residual 180.00 145.91 34.09 0 5.00e+00 4.00e-02 4.65e+01 ... (remaining 33777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 6794 0.063 - 0.126: 1853 0.126 - 0.189: 376 0.189 - 0.252: 37 0.252 - 0.315: 30 Chirality restraints: 9090 Sorted by residual: chirality pdb=" CA SER D 266 " pdb=" N SER D 266 " pdb=" C SER D 266 " pdb=" CB SER D 266 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA SER H 266 " pdb=" N SER H 266 " pdb=" C SER H 266 " pdb=" CB SER H 266 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA SER E 266 " pdb=" N SER E 266 " pdb=" C SER E 266 " pdb=" CB SER E 266 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 9087 not shown) Planarity restraints: 9690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 577 " 0.032 2.00e-02 2.50e+03 2.64e-02 1.39e+01 pdb=" CG TYR O 577 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR O 577 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR O 577 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR O 577 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR O 577 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR O 577 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR O 577 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 577 " 0.032 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR F 577 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR F 577 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR F 577 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 577 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR F 577 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR F 577 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 577 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 577 " 0.032 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR M 577 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR M 577 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR M 577 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR M 577 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR M 577 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR M 577 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR M 577 " 0.001 2.00e-02 2.50e+03 ... (remaining 9687 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 420 2.50 - 3.10: 42387 3.10 - 3.70: 80650 3.70 - 4.30: 120255 4.30 - 4.90: 205906 Nonbonded interactions: 449618 Sorted by model distance: nonbonded pdb=" OE1 GLU M 333 " pdb=" NH1 ARG M 506 " model vdw 1.901 2.520 nonbonded pdb=" OE1 GLU D 333 " pdb=" NH1 ARG D 506 " model vdw 1.901 2.520 nonbonded pdb=" OE1 GLU L 333 " pdb=" NH1 ARG L 506 " model vdw 1.901 2.520 nonbonded pdb=" OE1 GLU O 333 " pdb=" NH1 ARG O 506 " model vdw 1.901 2.520 nonbonded pdb=" OE1 GLU C 333 " pdb=" NH1 ARG C 506 " model vdw 1.901 2.520 ... (remaining 449613 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 individual isotropic 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 13.770 Check model and map are aligned: 0.600 Set scattering table: 0.360 Process input model: 102.920 Find NCS groups from input model: 2.910 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.009 0.070 55095 Z= 0.559 Angle : 1.021 10.683 74745 Z= 0.578 Chirality : 0.062 0.315 9090 Planarity : 0.005 0.055 9690 Dihedral : 11.516 82.747 20550 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.09 % Favored : 95.26 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.95 (0.08), residues: 6960 helix: -3.23 (0.09), residues: 1950 sheet: -0.82 (0.08), residues: 3090 loop : -1.98 (0.11), residues: 1920 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 869 time to evaluate : 4.596 Fit side-chains outliers start: 30 outliers final: 22 residues processed: 892 average time/residue: 0.5488 time to fit residues: 803.5883 Evaluate side-chains 614 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 592 time to evaluate : 4.650 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.5711 time to fit residues: 26.5378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 595 optimal weight: 1.9990 chunk 534 optimal weight: 1.9990 chunk 296 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 360 optimal weight: 0.3980 chunk 285 optimal weight: 5.9990 chunk 552 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 336 optimal weight: 9.9990 chunk 411 optimal weight: 0.9980 chunk 640 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN A 368 GLN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN B 368 GLN B 436 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 GLN C 335 GLN C 368 GLN C 436 ASN C 475 ASN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN D 335 GLN D 368 GLN D 436 ASN ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 GLN E 335 GLN E 368 GLN ** E 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN ** F 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 GLN F 335 GLN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** G 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 GLN G 308 GLN G 368 GLN G 475 ASN G 486 GLN H 188 GLN ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 GLN H 335 GLN H 368 GLN H 475 ASN H 486 GLN ** I 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 308 GLN I 368 GLN ** I 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 GLN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 GLN ** J 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN J 368 GLN J 475 ASN J 486 GLN K 188 GLN ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 GLN K 308 GLN K 335 GLN K 368 GLN K 475 ASN ** L 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 GLN ** L 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 308 GLN L 335 GLN L 368 GLN L 475 ASN ** M 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 GLN ** M 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 368 GLN M 475 ASN ** N 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 308 GLN N 335 GLN N 368 GLN N 475 ASN ** O 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 188 GLN ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 308 GLN O 335 GLN O 368 GLN ** O 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 55095 Z= 0.250 Angle : 0.690 8.046 74745 Z= 0.368 Chirality : 0.049 0.184 9090 Planarity : 0.006 0.039 9690 Dihedral : 6.094 23.912 7530 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.00 % Favored : 97.79 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -1.39 (0.09), residues: 6960 helix: -1.11 (0.10), residues: 1890 sheet: -0.40 (0.08), residues: 3015 loop : -1.14 (0.13), residues: 2055 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 770 time to evaluate : 4.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 35 residues processed: 842 average time/residue: 0.5262 time to fit residues: 755.8332 Evaluate side-chains 580 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 545 time to evaluate : 4.610 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4030 time to fit residues: 33.4835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 355 optimal weight: 0.8980 chunk 198 optimal weight: 10.0000 chunk 532 optimal weight: 4.9990 chunk 435 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 641 optimal weight: 0.9990 chunk 692 optimal weight: 2.9990 chunk 571 optimal weight: 9.9990 chunk 636 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 514 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN A 324 GLN A 341 ASN A 475 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 436 ASN ** E 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 GLN ** G 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 324 GLN ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 GLN H 324 GLN H 436 ASN ** H 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 324 GLN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 590 GLN ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 ASN ** K 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 257 ASN L 308 GLN L 475 ASN ** M 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 308 GLN ** M 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 486 GLN ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 335 GLN ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 257 ASN ** O 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 341 ASN ** O 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 55095 Z= 0.271 Angle : 0.637 9.214 74745 Z= 0.338 Chirality : 0.047 0.195 9090 Planarity : 0.005 0.042 9690 Dihedral : 5.472 20.651 7530 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.91 % Favored : 97.87 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.86 (0.09), residues: 6960 helix: 0.06 (0.11), residues: 1890 sheet: -0.49 (0.08), residues: 3015 loop : -0.98 (0.13), residues: 2055 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 579 time to evaluate : 4.597 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 42 residues processed: 645 average time/residue: 0.4742 time to fit residues: 536.6778 Evaluate side-chains 546 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 504 time to evaluate : 4.606 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4021 time to fit residues: 38.1824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 633 optimal weight: 1.9990 chunk 482 optimal weight: 3.9990 chunk 332 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 chunk 430 optimal weight: 9.9990 chunk 643 optimal weight: 0.9990 chunk 681 optimal weight: 0.8980 chunk 336 optimal weight: 20.0000 chunk 610 optimal weight: 0.0980 chunk 183 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 GLN F 214 ASN F 335 GLN F 365 ASN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN O 257 ASN ** O 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 55095 Z= 0.253 Angle : 0.603 9.897 74745 Z= 0.318 Chirality : 0.046 0.220 9090 Planarity : 0.005 0.043 9690 Dihedral : 5.129 18.359 7530 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.51 (0.10), residues: 6960 helix: 0.68 (0.12), residues: 1920 sheet: -0.50 (0.09), residues: 3015 loop : -0.76 (0.14), residues: 2025 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 548 time to evaluate : 4.811 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 51 residues processed: 629 average time/residue: 0.4800 time to fit residues: 531.3100 Evaluate side-chains 553 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 502 time to evaluate : 4.717 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.3775 time to fit residues: 43.4105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 567 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 507 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 581 optimal weight: 3.9990 chunk 471 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 347 optimal weight: 0.8980 chunk 611 optimal weight: 30.0000 chunk 171 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 335 GLN B 365 ASN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 GLN C 308 GLN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN C 475 ASN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 GLN D 335 GLN D 473 GLN D 475 ASN ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 GLN E 475 ASN ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN F 257 ASN F 324 GLN F 365 ASN F 475 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 ASN G 308 GLN G 475 ASN G 509 GLN ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 GLN H 475 ASN I 214 ASN I 308 GLN ** I 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 GLN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 ASN ** L 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 335 GLN L 475 ASN L 504 ASN ** M 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 308 GLN ** N 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 308 GLN ** O 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 335 GLN O 473 GLN O 475 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 55095 Z= 0.416 Angle : 0.661 10.889 74745 Z= 0.347 Chirality : 0.049 0.198 9090 Planarity : 0.005 0.047 9690 Dihedral : 5.283 20.131 7530 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.25 % Favored : 96.74 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.62 (0.10), residues: 6960 helix: 0.76 (0.12), residues: 1905 sheet: -0.64 (0.09), residues: 3015 loop : -0.86 (0.13), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 532 time to evaluate : 4.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 48 residues processed: 609 average time/residue: 0.4875 time to fit residues: 522.2123 Evaluate side-chains 548 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 500 time to evaluate : 4.746 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.3980 time to fit residues: 43.3638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 229 optimal weight: 0.9980 chunk 613 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 400 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 682 optimal weight: 0.9980 chunk 566 optimal weight: 20.0000 chunk 315 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 chunk 225 optimal weight: 0.5980 chunk 358 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 335 GLN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN D 308 GLN D 335 GLN D 365 ASN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 GLN ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN F 257 ASN F 365 ASN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN J 214 ASN J 308 GLN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 ASN ** K 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 335 GLN ** L 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 308 GLN ** M 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 365 ASN ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN O 335 GLN O 436 ASN ** O 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 55095 Z= 0.224 Angle : 0.571 9.541 74745 Z= 0.301 Chirality : 0.045 0.160 9090 Planarity : 0.005 0.045 9690 Dihedral : 4.905 17.862 7530 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.35 (0.10), residues: 6960 helix: 1.07 (0.12), residues: 1935 sheet: -0.58 (0.09), residues: 3015 loop : -0.66 (0.14), residues: 2010 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 559 time to evaluate : 4.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 17 residues processed: 601 average time/residue: 0.4984 time to fit residues: 526.2551 Evaluate side-chains 534 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 517 time to evaluate : 4.602 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3903 time to fit residues: 19.1822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 657 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 388 optimal weight: 8.9990 chunk 498 optimal weight: 1.9990 chunk 385 optimal weight: 0.5980 chunk 574 optimal weight: 8.9990 chunk 380 optimal weight: 9.9990 chunk 679 optimal weight: 4.9990 chunk 425 optimal weight: 9.9990 chunk 414 optimal weight: 2.9990 chunk 313 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 335 GLN A 341 ASN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 335 GLN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN C 335 GLN C 475 ASN D 214 ASN D 335 GLN D 365 ASN D 475 ASN ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 ASN E 475 ASN F 214 ASN ** F 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 ASN G 475 ASN ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 475 ASN I 214 ASN I 324 GLN J 214 ASN J 475 ASN J 509 GLN K 214 ASN K 475 ASN ** L 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 475 ASN ** M 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 GLN ** M 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 365 ASN ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN ** O 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 335 GLN O 475 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 55095 Z= 0.364 Angle : 0.630 13.485 74745 Z= 0.329 Chirality : 0.047 0.179 9090 Planarity : 0.005 0.047 9690 Dihedral : 5.072 19.502 7530 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.15 % Favored : 96.68 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.40 (0.10), residues: 6960 helix: 1.05 (0.12), residues: 1935 sheet: -0.56 (0.09), residues: 2925 loop : -0.80 (0.13), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 511 time to evaluate : 4.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 54 residues processed: 578 average time/residue: 0.4869 time to fit residues: 492.0790 Evaluate side-chains 544 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 490 time to evaluate : 4.646 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.3840 time to fit residues: 46.1780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 420 optimal weight: 0.6980 chunk 271 optimal weight: 0.6980 chunk 405 optimal weight: 0.5980 chunk 204 optimal weight: 0.0870 chunk 133 optimal weight: 0.0170 chunk 131 optimal weight: 0.7980 chunk 432 optimal weight: 20.0000 chunk 462 optimal weight: 0.8980 chunk 335 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 534 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 335 GLN A 475 ASN B 335 GLN B 365 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 365 ASN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN E 214 ASN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 GLN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 ASN H 214 ASN H 335 GLN H 365 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 509 GLN K 341 ASN ** K 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 365 ASN ** L 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 214 ASN ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN O 335 GLN O 436 ASN ** O 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 55095 Z= 0.155 Angle : 0.544 12.345 74745 Z= 0.284 Chirality : 0.044 0.153 9090 Planarity : 0.004 0.046 9690 Dihedral : 4.634 16.960 7530 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.10 (0.10), residues: 6960 helix: 1.33 (0.12), residues: 1935 sheet: -0.41 (0.09), residues: 2925 loop : -0.64 (0.14), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 568 time to evaluate : 4.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 13 residues processed: 602 average time/residue: 0.4913 time to fit residues: 521.6603 Evaluate side-chains 531 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 518 time to evaluate : 4.639 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4033 time to fit residues: 16.4895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 618 optimal weight: 10.0000 chunk 650 optimal weight: 1.9990 chunk 593 optimal weight: 1.9990 chunk 633 optimal weight: 0.5980 chunk 381 optimal weight: 1.9990 chunk 275 optimal weight: 0.6980 chunk 497 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 chunk 572 optimal weight: 9.9990 chunk 598 optimal weight: 0.9990 chunk 631 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN B 365 ASN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN C 335 GLN C 475 ASN D 335 GLN ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN F 365 ASN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 ASN H 214 ASN H 335 GLN H 365 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 509 GLN K 475 ASN ** L 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 365 ASN L 475 ASN ** M 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 365 ASN ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 214 ASN ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 335 GLN O 436 ASN O 475 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 55095 Z= 0.221 Angle : 0.568 12.490 74745 Z= 0.296 Chirality : 0.045 0.168 9090 Planarity : 0.005 0.045 9690 Dihedral : 4.682 17.185 7530 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.50 % Favored : 97.33 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.12 (0.10), residues: 6960 helix: 1.31 (0.12), residues: 1920 sheet: -0.40 (0.09), residues: 2925 loop : -0.67 (0.14), residues: 2115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 517 time to evaluate : 4.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 541 average time/residue: 0.5097 time to fit residues: 483.2867 Evaluate side-chains 522 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 510 time to evaluate : 4.597 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4086 time to fit residues: 15.7803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 415 optimal weight: 0.6980 chunk 669 optimal weight: 8.9990 chunk 408 optimal weight: 0.5980 chunk 317 optimal weight: 0.0770 chunk 465 optimal weight: 0.7980 chunk 702 optimal weight: 0.6980 chunk 646 optimal weight: 0.6980 chunk 559 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 432 optimal weight: 2.9990 chunk 342 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN B 365 ASN C 475 ASN D 335 GLN D 475 ASN F 365 ASN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 473 GLN G 475 ASN H 365 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 ASN L 214 ASN L 475 ASN ** M 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 365 ASN ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 335 GLN O 436 ASN O 475 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 55095 Z= 0.175 Angle : 0.546 12.128 74745 Z= 0.284 Chirality : 0.044 0.162 9090 Planarity : 0.004 0.046 9690 Dihedral : 4.543 17.207 7530 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.43 % Favored : 97.40 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.00 (0.10), residues: 6960 helix: 1.41 (0.12), residues: 1920 sheet: -0.33 (0.09), residues: 2925 loop : -0.61 (0.14), residues: 2115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 530 time to evaluate : 4.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 541 average time/residue: 0.4884 time to fit residues: 468.0502 Evaluate side-chains 517 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 512 time to evaluate : 4.614 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3840 time to fit residues: 10.3179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 444 optimal weight: 2.9990 chunk 595 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 515 optimal weight: 4.9990 chunk 82 optimal weight: 0.0070 chunk 155 optimal weight: 0.7980 chunk 560 optimal weight: 0.9980 chunk 234 optimal weight: 0.0870 chunk 575 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN D 335 GLN ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 ASN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 ASN L 214 ASN L 365 ASN L 475 ASN ** M 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 257 ASN O 436 ASN ** O 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.213054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.130783 restraints weight = 53529.892| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.02 r_work: 0.3156 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 55095 Z= 0.182 Angle : 0.549 12.145 74745 Z= 0.286 Chirality : 0.044 0.160 9090 Planarity : 0.004 0.045 9690 Dihedral : 4.518 17.466 7530 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.40 % Favored : 97.43 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.04 (0.10), residues: 6960 helix: 1.44 (0.12), residues: 1920 sheet: -0.29 (0.09), residues: 2925 loop : -0.63 (0.14), residues: 2115 =============================================================================== Job complete usr+sys time: 11297.90 seconds wall clock time: 199 minutes 55.33 seconds (11995.33 seconds total)