Starting phenix.real_space_refine on Wed Sep 25 05:42:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/09_2024/6i1x_0326_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/09_2024/6i1x_0326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/09_2024/6i1x_0326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/09_2024/6i1x_0326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/09_2024/6i1x_0326_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/09_2024/6i1x_0326_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.009 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 150 5.16 5 C 34155 2.51 5 N 9675 2.21 5 O 10935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 54915 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "D" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "E" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "F" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "G" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "H" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "I" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "J" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "K" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "L" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "M" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "N" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "O" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Time building chain proxies: 23.20, per 1000 atoms: 0.42 Number of scatterers: 54915 At special positions: 0 Unit cell: (158.51, 157.3, 182.71, 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 150 16.00 O 10935 8.00 N 9675 7.00 C 34155 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 - 3.00 Amino acid : True - 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: 9.90 Conformation dependent library (CDL) restraints added in 5.4 seconds 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13290 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 0 sheets defined 32.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 111 through 114 removed outlier: 3.723A pdb=" N GLU A 114 " --> pdb=" O SER A 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 115 through 124 Processing helix chain 'A' and resid 145 through 163 removed outlier: 3.888A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 220 through 234 removed outlier: 3.596A pdb=" N GLN A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.852A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 578 through 607 removed outlier: 3.655A pdb=" N GLY A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 removed outlier: 3.729A pdb=" N GLU B 114 " --> pdb=" O SER B 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 115 through 124 Processing helix chain 'B' and resid 145 through 163 removed outlier: 3.910A pdb=" N GLY B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 220 through 235 removed outlier: 3.589A pdb=" N GLN B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.851A pdb=" N GLU B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 323 Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 543 through 547 Processing helix chain 'B' and resid 549 through 554 Processing helix chain 'B' and resid 578 through 607 removed outlier: 3.658A pdb=" N GLY B 583 " --> pdb=" O ASN B 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 588 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 removed outlier: 3.736A pdb=" N GLU C 114 " --> pdb=" O SER C 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 115 through 124 Processing helix chain 'C' and resid 145 through 163 removed outlier: 3.896A pdb=" N GLY C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 220 through 234 removed outlier: 3.590A pdb=" N GLN C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 removed outlier: 3.847A pdb=" N GLU C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 323 Processing helix chain 'C' and resid 366 through 377 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 549 through 554 Processing helix chain 'C' and resid 578 through 607 removed outlier: 3.659A pdb=" N GLY C 583 " --> pdb=" O ASN C 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 588 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR C 605 " --> pdb=" O ALA C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 114 removed outlier: 3.720A pdb=" N GLU D 114 " --> pdb=" O SER D 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 111 through 114' Processing helix chain 'D' and resid 115 through 124 Processing helix chain 'D' and resid 145 through 163 removed outlier: 3.892A pdb=" N GLY D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 220 through 234 removed outlier: 3.601A pdb=" N GLN D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 removed outlier: 3.837A pdb=" N GLU D 259 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 323 Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 383 through 390 Processing helix chain 'D' and resid 543 through 547 Processing helix chain 'D' and resid 549 through 554 Processing helix chain 'D' and resid 578 through 607 removed outlier: 3.659A pdb=" N GLY D 583 " --> pdb=" O ASN D 579 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 588 " --> pdb=" O ILE D 584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 114 removed outlier: 3.725A pdb=" N GLU E 114 " --> pdb=" O SER E 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 111 through 114' Processing helix chain 'E' and resid 115 through 124 Processing helix chain 'E' and resid 145 through 163 removed outlier: 3.887A pdb=" N GLY E 163 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 186 Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 220 through 234 removed outlier: 3.625A pdb=" N GLN E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.805A pdb=" N GLU E 259 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL E 264 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 323 Processing helix chain 'E' and resid 366 through 377 Processing helix chain 'E' and resid 383 through 390 Processing helix chain 'E' and resid 543 through 547 Processing helix chain 'E' and resid 549 through 554 Processing helix chain 'E' and resid 578 through 607 removed outlier: 3.644A pdb=" N GLY E 583 " --> pdb=" O ASN E 579 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS E 588 " --> pdb=" O ILE E 584 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR E 605 " --> pdb=" O ALA E 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 114 removed outlier: 3.713A pdb=" N GLU F 114 " --> pdb=" O SER F 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 111 through 114' Processing helix chain 'F' and resid 115 through 124 Processing helix chain 'F' and resid 145 through 163 removed outlier: 3.887A pdb=" N GLY F 163 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 186 Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 220 through 234 removed outlier: 3.632A pdb=" N GLN F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.822A pdb=" N GLU F 259 " --> pdb=" O LYS F 255 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY F 263 " --> pdb=" O GLU F 259 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL F 264 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 323 Processing helix chain 'F' and resid 366 through 377 Processing helix chain 'F' and resid 383 through 390 Processing helix chain 'F' and resid 543 through 547 Processing helix chain 'F' and resid 549 through 554 Processing helix chain 'F' and resid 578 through 607 removed outlier: 3.665A pdb=" N GLY F 583 " --> pdb=" O ASN F 579 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS F 588 " --> pdb=" O ILE F 584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR F 605 " --> pdb=" O ALA F 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 114 removed outlier: 3.704A pdb=" N GLU G 114 " --> pdb=" O SER G 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 111 through 114' Processing helix chain 'G' and resid 115 through 124 Processing helix chain 'G' and resid 145 through 163 removed outlier: 3.878A pdb=" N GLY G 163 " --> pdb=" O VAL G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 186 Processing helix chain 'G' and resid 199 through 203 Processing helix chain 'G' and resid 220 through 234 removed outlier: 3.644A pdb=" N GLN G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 266 removed outlier: 3.804A pdb=" N GLU G 259 " --> pdb=" O LYS G 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY G 263 " --> pdb=" O GLU G 259 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL G 264 " --> pdb=" O VAL G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 323 Processing helix chain 'G' and resid 366 through 377 Processing helix chain 'G' and resid 383 through 390 Processing helix chain 'G' and resid 543 through 547 Processing helix chain 'G' and resid 549 through 554 Processing helix chain 'G' and resid 578 through 607 removed outlier: 3.660A pdb=" N GLY G 583 " --> pdb=" O ASN G 579 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS G 588 " --> pdb=" O ILE G 584 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR G 605 " --> pdb=" O ALA G 601 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 114 removed outlier: 3.713A pdb=" N GLU H 114 " --> pdb=" O SER H 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 114' Processing helix chain 'H' and resid 115 through 124 Processing helix chain 'H' and resid 145 through 163 removed outlier: 3.907A pdb=" N GLY H 163 " --> pdb=" O VAL H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 186 Processing helix chain 'H' and resid 199 through 203 Processing helix chain 'H' and resid 220 through 234 removed outlier: 3.623A pdb=" N GLN H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 266 removed outlier: 3.840A pdb=" N GLU H 259 " --> pdb=" O LYS H 255 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY H 263 " --> pdb=" O GLU H 259 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL H 264 " --> pdb=" O VAL H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 323 Processing helix chain 'H' and resid 366 through 377 Processing helix chain 'H' and resid 383 through 390 Processing helix chain 'H' and resid 543 through 547 Processing helix chain 'H' and resid 549 through 554 Processing helix chain 'H' and resid 578 through 607 removed outlier: 3.662A pdb=" N GLY H 583 " --> pdb=" O ASN H 579 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 588 " --> pdb=" O ILE H 584 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 605 " --> pdb=" O ALA H 601 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 114 removed outlier: 3.758A pdb=" N GLU I 114 " --> pdb=" O SER I 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 111 through 114' Processing helix chain 'I' and resid 115 through 124 Processing helix chain 'I' and resid 145 through 163 removed outlier: 3.863A pdb=" N GLY I 163 " --> pdb=" O VAL I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 186 Processing helix chain 'I' and resid 199 through 203 Processing helix chain 'I' and resid 220 through 235 removed outlier: 3.637A pdb=" N GLN I 229 " --> pdb=" O ALA I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 266 removed outlier: 3.833A pdb=" N GLU I 259 " --> pdb=" O LYS I 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I 260 " --> pdb=" O ASP I 256 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY I 263 " --> pdb=" O GLU I 259 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL I 264 " --> pdb=" O VAL I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 323 Processing helix chain 'I' and resid 366 through 377 removed outlier: 3.512A pdb=" N VAL I 370 " --> pdb=" O GLY I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 390 Processing helix chain 'I' and resid 543 through 547 Processing helix chain 'I' and resid 549 through 554 Processing helix chain 'I' and resid 578 through 607 removed outlier: 3.673A pdb=" N GLY I 583 " --> pdb=" O ASN I 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS I 588 " --> pdb=" O ILE I 584 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR I 605 " --> pdb=" O ALA I 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 114 removed outlier: 3.744A pdb=" N GLU J 114 " --> pdb=" O SER J 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 111 through 114' Processing helix chain 'J' and resid 115 through 124 Processing helix chain 'J' and resid 145 through 163 removed outlier: 3.897A pdb=" N GLY J 163 " --> pdb=" O VAL J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 186 Processing helix chain 'J' and resid 199 through 203 Processing helix chain 'J' and resid 220 through 235 removed outlier: 3.587A pdb=" N GLN J 229 " --> pdb=" O ALA J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 266 removed outlier: 3.845A pdb=" N GLU J 259 " --> pdb=" O LYS J 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL J 260 " --> pdb=" O ASP J 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY J 263 " --> pdb=" O GLU J 259 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL J 264 " --> pdb=" O VAL J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 323 Processing helix chain 'J' and resid 366 through 377 Processing helix chain 'J' and resid 383 through 390 Processing helix chain 'J' and resid 543 through 547 Processing helix chain 'J' and resid 549 through 554 Processing helix chain 'J' and resid 578 through 607 removed outlier: 3.655A pdb=" N GLY J 583 " --> pdb=" O ASN J 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS J 588 " --> pdb=" O ILE J 584 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR J 605 " --> pdb=" O ALA J 601 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 114 removed outlier: 3.720A pdb=" N GLU K 114 " --> pdb=" O SER K 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 111 through 114' Processing helix chain 'K' and resid 115 through 124 Processing helix chain 'K' and resid 145 through 163 removed outlier: 3.899A pdb=" N GLY K 163 " --> pdb=" O VAL K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 186 Processing helix chain 'K' and resid 199 through 203 Processing helix chain 'K' and resid 220 through 234 removed outlier: 3.601A pdb=" N GLN K 229 " --> pdb=" O ALA K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 266 removed outlier: 3.840A pdb=" N GLU K 259 " --> pdb=" O LYS K 255 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL K 260 " --> pdb=" O ASP K 256 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY K 263 " --> pdb=" O GLU K 259 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL K 264 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 323 Processing helix chain 'K' and resid 366 through 377 Processing helix chain 'K' and resid 383 through 390 Processing helix chain 'K' and resid 543 through 547 Processing helix chain 'K' and resid 549 through 554 Processing helix chain 'K' and resid 578 through 607 removed outlier: 3.656A pdb=" N GLY K 583 " --> pdb=" O ASN K 579 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS K 588 " --> pdb=" O ILE K 584 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR K 605 " --> pdb=" O ALA K 601 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 114 removed outlier: 3.729A pdb=" N GLU L 114 " --> pdb=" O SER L 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 111 through 114' Processing helix chain 'L' and resid 115 through 124 Processing helix chain 'L' and resid 145 through 163 removed outlier: 3.901A pdb=" N GLY L 163 " --> pdb=" O VAL L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 186 Processing helix chain 'L' and resid 199 through 203 Processing helix chain 'L' and resid 220 through 235 removed outlier: 3.594A pdb=" N GLN L 229 " --> pdb=" O ALA L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 253 through 266 removed outlier: 3.845A pdb=" N GLU L 259 " --> pdb=" O LYS L 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 260 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY L 263 " --> pdb=" O GLU L 259 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL L 264 " --> pdb=" O VAL L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 323 Processing helix chain 'L' and resid 366 through 377 Processing helix chain 'L' and resid 383 through 390 Processing helix chain 'L' and resid 543 through 547 Processing helix chain 'L' and resid 549 through 554 Processing helix chain 'L' and resid 578 through 607 removed outlier: 3.654A pdb=" N GLY L 583 " --> pdb=" O ASN L 579 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS L 588 " --> pdb=" O ILE L 584 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR L 605 " --> pdb=" O ALA L 601 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 114 removed outlier: 3.735A pdb=" N GLU M 114 " --> pdb=" O SER M 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 111 through 114' Processing helix chain 'M' and resid 115 through 124 Processing helix chain 'M' and resid 145 through 163 removed outlier: 3.903A pdb=" N GLY M 163 " --> pdb=" O VAL M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 186 Processing helix chain 'M' and resid 199 through 203 Processing helix chain 'M' and resid 220 through 235 removed outlier: 3.594A pdb=" N GLN M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 266 removed outlier: 3.842A pdb=" N GLU M 259 " --> pdb=" O LYS M 255 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL M 260 " --> pdb=" O ASP M 256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY M 263 " --> pdb=" O GLU M 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL M 264 " --> pdb=" O VAL M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 323 Processing helix chain 'M' and resid 366 through 377 Processing helix chain 'M' and resid 383 through 390 Processing helix chain 'M' and resid 543 through 547 Processing helix chain 'M' and resid 549 through 554 Processing helix chain 'M' and resid 578 through 607 removed outlier: 3.654A pdb=" N GLY M 583 " --> pdb=" O ASN M 579 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS M 588 " --> pdb=" O ILE M 584 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR M 605 " --> pdb=" O ALA M 601 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 114 removed outlier: 3.722A pdb=" N GLU N 114 " --> pdb=" O SER N 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 111 through 114' Processing helix chain 'N' and resid 115 through 124 Processing helix chain 'N' and resid 145 through 163 removed outlier: 3.895A pdb=" N GLY N 163 " --> pdb=" O VAL N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 186 Processing helix chain 'N' and resid 199 through 203 Processing helix chain 'N' and resid 220 through 234 removed outlier: 3.600A pdb=" N GLN N 229 " --> pdb=" O ALA N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 266 removed outlier: 3.839A pdb=" N GLU N 259 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL N 260 " --> pdb=" O ASP N 256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY N 263 " --> pdb=" O GLU N 259 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL N 264 " --> pdb=" O VAL N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 323 Processing helix chain 'N' and resid 366 through 377 Processing helix chain 'N' and resid 383 through 390 Processing helix chain 'N' and resid 543 through 547 Processing helix chain 'N' and resid 549 through 554 Processing helix chain 'N' and resid 578 through 607 removed outlier: 3.657A pdb=" N GLY N 583 " --> pdb=" O ASN N 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS N 588 " --> pdb=" O ILE N 584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR N 605 " --> pdb=" O ALA N 601 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 114 removed outlier: 3.724A pdb=" N GLU O 114 " --> pdb=" O SER O 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 111 through 114' Processing helix chain 'O' and resid 115 through 124 Processing helix chain 'O' and resid 145 through 163 removed outlier: 3.899A pdb=" N GLY O 163 " --> pdb=" O VAL O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 199 through 203 Processing helix chain 'O' and resid 220 through 234 removed outlier: 3.598A pdb=" N GLN O 229 " --> pdb=" O ALA O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 266 removed outlier: 3.839A pdb=" N GLU O 259 " --> pdb=" O LYS O 255 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL O 260 " --> pdb=" O ASP O 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY O 263 " --> pdb=" O GLU O 259 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL O 264 " --> pdb=" O VAL O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 323 Processing helix chain 'O' and resid 366 through 377 Processing helix chain 'O' and resid 383 through 390 Processing helix chain 'O' and resid 543 through 547 Processing helix chain 'O' and resid 549 through 554 Processing helix chain 'O' and resid 578 through 607 removed outlier: 3.655A pdb=" N GLY O 583 " --> pdb=" O ASN O 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS O 588 " --> pdb=" O ILE O 584 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR O 605 " --> pdb=" O ALA O 601 " (cutoff:3.500A) 1459 hydrogen bonds defined for protein. 4062 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: 11.29 Time building geometry restraints manager: 11.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11082 1.32 - 1.45: 11247 1.45 - 1.58: 32856 1.58 - 1.70: 0 1.70 - 1.83: 300 Bond restraints: 55485 Sorted by residual: bond pdb=" CA TYR F 174 " pdb=" C TYR F 174 " ideal model delta sigma weight residual 1.520 1.545 -0.026 4.80e-03 4.34e+04 2.89e+01 bond pdb=" CA TYR G 174 " pdb=" C TYR G 174 " ideal model delta sigma weight residual 1.520 1.544 -0.025 4.80e-03 4.34e+04 2.65e+01 bond pdb=" CA TYR N 174 " pdb=" C TYR N 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.60e+01 bond pdb=" CA TYR K 174 " pdb=" C TYR K 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.59e+01 bond pdb=" CA TYR D 174 " pdb=" C TYR D 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.59e+01 ... (remaining 55480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 53796 1.88 - 3.76: 18358 3.76 - 5.64: 2776 5.64 - 7.52: 246 7.52 - 9.40: 79 Bond angle restraints: 75255 Sorted by residual: angle pdb=" N PRO I 609 " pdb=" CA PRO I 609 " pdb=" CB PRO I 609 " ideal model delta sigma weight residual 103.25 94.24 9.01 1.05e+00 9.07e-01 7.36e+01 angle pdb=" N PRO D 609 " pdb=" CA PRO D 609 " pdb=" CB PRO D 609 " ideal model delta sigma weight residual 103.25 94.43 8.82 1.05e+00 9.07e-01 7.06e+01 angle pdb=" N PRO H 609 " pdb=" CA PRO H 609 " pdb=" CB PRO H 609 " ideal model delta sigma weight residual 103.25 94.45 8.80 1.05e+00 9.07e-01 7.03e+01 angle pdb=" N PRO B 609 " pdb=" CA PRO B 609 " pdb=" CB PRO B 609 " ideal model delta sigma weight residual 103.25 94.49 8.76 1.05e+00 9.07e-01 6.96e+01 angle pdb=" N PRO C 609 " pdb=" CA PRO C 609 " pdb=" CB PRO C 609 " ideal model delta sigma weight residual 103.25 94.50 8.75 1.05e+00 9.07e-01 6.94e+01 ... (remaining 75250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 30582 18.10 - 36.19: 2588 36.19 - 54.29: 609 54.29 - 72.39: 121 72.39 - 90.49: 30 Dihedral angle restraints: 33930 sinusoidal: 13230 harmonic: 20700 Sorted by residual: dihedral pdb=" CA LYS I 189 " pdb=" C LYS I 189 " pdb=" N ASP I 190 " pdb=" CA ASP I 190 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LYS H 189 " pdb=" C LYS H 189 " pdb=" N ASP H 190 " pdb=" CA ASP H 190 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA LYS G 189 " pdb=" C LYS G 189 " pdb=" N ASP G 190 " pdb=" CA ASP G 190 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 33927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3853 0.061 - 0.123: 3239 0.123 - 0.184: 1572 0.184 - 0.245: 391 0.245 - 0.306: 65 Chirality restraints: 9120 Sorted by residual: chirality pdb=" CA LYS E 250 " pdb=" N LYS E 250 " pdb=" C LYS E 250 " pdb=" CB LYS E 250 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LYS F 250 " pdb=" N LYS F 250 " pdb=" C LYS F 250 " pdb=" CB LYS F 250 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LYS L 250 " pdb=" N LYS L 250 " pdb=" C LYS L 250 " pdb=" CB LYS L 250 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 9117 not shown) Planarity restraints: 9855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 613 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C VAL F 613 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL F 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU F 614 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 613 " 0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C VAL B 613 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL B 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU B 614 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 613 " 0.017 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C VAL H 613 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL H 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU H 614 " 0.022 2.00e-02 2.50e+03 ... (remaining 9852 not shown) Histogram of nonbonded interaction distances: 0.46 - 1.35: 5 1.35 - 2.23: 94 2.23 - 3.12: 45107 3.12 - 4.01: 145267 4.01 - 4.90: 262893 Warning: very small nonbonded interaction distances. Nonbonded interactions: 453366 Sorted by model distance: nonbonded pdb=" CG2 VAL H 139 " pdb=" C ALA I 162 " model vdw 0.458 3.690 nonbonded pdb=" CB VAL H 139 " pdb=" O ALA I 162 " model vdw 0.818 3.470 nonbonded pdb=" CG2 VAL H 139 " pdb=" O ALA I 162 " model vdw 1.091 3.460 nonbonded pdb=" CG2 VAL H 139 " pdb=" N GLY I 163 " model vdw 1.289 3.540 nonbonded pdb=" ND2 ASN I 138 " pdb=" O THR J 198 " model vdw 1.323 3.120 ... (remaining 453361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.530 Check model and map are aligned: 0.310 Set scattering table: 0.390 Process input model: 81.820 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.280 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:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3237 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.061 55485 Z= 0.838 Angle : 1.810 9.397 75255 Z= 1.296 Chirality : 0.098 0.306 9120 Planarity : 0.008 0.072 9855 Dihedral : 14.937 90.487 20640 Min Nonbonded Distance : 0.458 Molprobity Statistics. All-atom Clashscore : 50.06 Ramachandran Plot: Outliers : 1.89 % Allowed : 7.50 % Favored : 90.61 % Rotamer: Outliers : 4.35 % Allowed : 8.17 % Favored : 87.48 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.08), residues: 7200 helix: -2.95 (0.08), residues: 1965 sheet: -1.10 (0.10), residues: 2175 loop : -2.72 (0.08), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.006 TRP I 350 HIS 0.006 0.003 HIS H 133 PHE 0.035 0.007 PHE E 247 TYR 0.039 0.007 TYR H 134 ARG 0.009 0.001 ARG F 576 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1804 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1541 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.5898 (t) cc_final: 0.4828 (t) REVERT: A 211 ARG cc_start: 0.4395 (mtt180) cc_final: 0.4192 (ttt180) REVERT: A 229 GLN cc_start: 0.7222 (mt0) cc_final: 0.7018 (mm-40) REVERT: A 255 LYS cc_start: 0.6764 (tttt) cc_final: 0.6536 (mmtt) REVERT: A 259 GLU cc_start: 0.6116 (mm-30) cc_final: 0.5626 (mt-10) REVERT: A 298 GLU cc_start: 0.6169 (tt0) cc_final: 0.5812 (pm20) REVERT: A 312 MET cc_start: 0.7262 (tpp) cc_final: 0.6962 (mmm) REVERT: A 345 ASN cc_start: 0.6678 (p0) cc_final: 0.6193 (p0) REVERT: A 407 MET cc_start: 0.3897 (ttp) cc_final: 0.3218 (tmm) REVERT: A 413 SER cc_start: 0.5500 (m) cc_final: 0.5171 (t) REVERT: A 433 GLU cc_start: 0.6624 (pt0) cc_final: 0.6287 (mt-10) REVERT: A 478 GLU cc_start: 0.7534 (tp30) cc_final: 0.7005 (pp20) REVERT: A 487 GLU cc_start: 0.4338 (tt0) cc_final: 0.4085 (tp30) REVERT: A 534 THR cc_start: 0.7041 (m) cc_final: 0.6302 (m) REVERT: A 550 LEU cc_start: 0.7533 (mt) cc_final: 0.7132 (tp) REVERT: A 553 LEU cc_start: 0.7238 (mt) cc_final: 0.6916 (mt) REVERT: A 558 SER cc_start: 0.3396 (t) cc_final: 0.2744 (m) REVERT: A 560 ASN cc_start: 0.6903 (t0) cc_final: 0.6640 (t0) REVERT: A 591 LEU cc_start: 0.8430 (tp) cc_final: 0.8174 (tp) REVERT: A 602 GLN cc_start: 0.5736 (mt0) cc_final: 0.5511 (tp40) REVERT: B 167 VAL cc_start: 0.6045 (t) cc_final: 0.5403 (t) REVERT: B 174 TYR cc_start: 0.4200 (m-80) cc_final: 0.3920 (m-80) REVERT: B 229 GLN cc_start: 0.6882 (mt0) cc_final: 0.6565 (mm-40) REVERT: B 312 MET cc_start: 0.7779 (tpp) cc_final: 0.7559 (mmm) REVERT: B 345 ASN cc_start: 0.6405 (p0) cc_final: 0.6085 (t0) REVERT: B 359 GLN cc_start: 0.6386 (tt0) cc_final: 0.5970 (tp40) REVERT: B 413 SER cc_start: 0.5064 (m) cc_final: 0.4641 (t) REVERT: B 433 GLU cc_start: 0.6281 (pt0) cc_final: 0.5772 (mp0) REVERT: B 461 ILE cc_start: 0.2494 (OUTLIER) cc_final: 0.2009 (pt) REVERT: B 478 GLU cc_start: 0.7408 (tp30) cc_final: 0.6958 (pp20) REVERT: B 535 LYS cc_start: 0.7736 (ttmt) cc_final: 0.7529 (tttp) REVERT: B 550 LEU cc_start: 0.7398 (mt) cc_final: 0.6814 (tt) REVERT: B 562 SER cc_start: 0.6415 (m) cc_final: 0.6054 (t) REVERT: B 579 ASN cc_start: 0.7270 (m-40) cc_final: 0.6862 (p0) REVERT: B 602 GLN cc_start: 0.7041 (mt0) cc_final: 0.6598 (tp40) REVERT: C 167 VAL cc_start: 0.6930 (t) cc_final: 0.6472 (t) REVERT: C 229 GLN cc_start: 0.7270 (mt0) cc_final: 0.6895 (mm-40) REVERT: C 312 MET cc_start: 0.7687 (tpp) cc_final: 0.7454 (mmm) REVERT: C 325 ARG cc_start: 0.6063 (ttt180) cc_final: 0.5832 (ttm110) REVERT: C 345 ASN cc_start: 0.6445 (p0) cc_final: 0.5918 (t0) REVERT: C 413 SER cc_start: 0.5241 (m) cc_final: 0.4691 (t) REVERT: C 429 MET cc_start: 0.3990 (mmm) cc_final: 0.2918 (mmm) REVERT: C 430 ASP cc_start: 0.3511 (p0) cc_final: 0.2516 (p0) REVERT: C 433 GLU cc_start: 0.6744 (pt0) cc_final: 0.6390 (mt-10) REVERT: C 461 ILE cc_start: 0.2834 (OUTLIER) cc_final: 0.2043 (pt) REVERT: C 463 ARG cc_start: 0.3204 (OUTLIER) cc_final: 0.2888 (mtp85) REVERT: C 503 LEU cc_start: 0.4588 (OUTLIER) cc_final: 0.4262 (mt) REVERT: C 535 LYS cc_start: 0.7612 (ttmt) cc_final: 0.7400 (tttp) REVERT: C 550 LEU cc_start: 0.7228 (mt) cc_final: 0.6808 (tt) REVERT: C 567 MET cc_start: 0.5010 (mmm) cc_final: 0.4806 (mmt) REVERT: C 579 ASN cc_start: 0.7525 (m-40) cc_final: 0.7051 (p0) REVERT: C 591 LEU cc_start: 0.8483 (tp) cc_final: 0.8259 (tp) REVERT: C 602 GLN cc_start: 0.7049 (mt0) cc_final: 0.6784 (tp40) REVERT: D 215 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7461 (p) REVERT: D 227 ILE cc_start: 0.7450 (mt) cc_final: 0.7203 (tp) REVERT: D 229 GLN cc_start: 0.7229 (mt0) cc_final: 0.7000 (mm-40) REVERT: D 259 GLU cc_start: 0.6188 (mm-30) cc_final: 0.5848 (mt-10) REVERT: D 312 MET cc_start: 0.7642 (tpp) cc_final: 0.7439 (mmm) REVERT: D 325 ARG cc_start: 0.6569 (ttt180) cc_final: 0.6263 (ttm170) REVERT: D 345 ASN cc_start: 0.6464 (p0) cc_final: 0.6211 (t0) REVERT: D 433 GLU cc_start: 0.6726 (pt0) cc_final: 0.6417 (mt-10) REVERT: D 463 ARG cc_start: 0.2642 (OUTLIER) cc_final: 0.2344 (mtp85) REVERT: D 475 GLN cc_start: 0.4699 (tt0) cc_final: 0.4286 (tm-30) REVERT: D 535 LYS cc_start: 0.7598 (ttmt) cc_final: 0.7352 (tttp) REVERT: D 550 LEU cc_start: 0.7339 (mt) cc_final: 0.6915 (tt) REVERT: D 562 SER cc_start: 0.6220 (m) cc_final: 0.5860 (t) REVERT: D 579 ASN cc_start: 0.7226 (m-40) cc_final: 0.6804 (p0) REVERT: D 602 GLN cc_start: 0.6813 (mt0) cc_final: 0.6566 (tp40) REVERT: E 190 ASP cc_start: -0.2286 (OUTLIER) cc_final: -0.3142 (m-30) REVERT: E 227 ILE cc_start: 0.7592 (mt) cc_final: 0.7298 (mm) REVERT: E 238 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.4930 (tp) REVERT: E 246 VAL cc_start: 0.7019 (t) cc_final: 0.6588 (p) REVERT: E 345 ASN cc_start: 0.6552 (p0) cc_final: 0.6330 (p0) REVERT: E 413 SER cc_start: 0.5873 (m) cc_final: 0.5558 (t) REVERT: E 433 GLU cc_start: 0.6246 (pt0) cc_final: 0.6013 (mt-10) REVERT: E 461 ILE cc_start: 0.3244 (OUTLIER) cc_final: 0.2368 (pt) REVERT: E 478 GLU cc_start: 0.7186 (tp30) cc_final: 0.6794 (pp20) REVERT: E 503 LEU cc_start: 0.4665 (OUTLIER) cc_final: 0.4020 (mt) REVERT: E 534 THR cc_start: 0.7699 (m) cc_final: 0.7352 (m) REVERT: E 535 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7327 (tttp) REVERT: E 579 ASN cc_start: 0.7110 (m-40) cc_final: 0.6801 (p0) REVERT: F 160 ASP cc_start: 0.6044 (t70) cc_final: 0.5828 (m-30) REVERT: F 174 TYR cc_start: 0.4414 (m-80) cc_final: 0.4160 (m-80) REVERT: F 215 VAL cc_start: 0.6449 (OUTLIER) cc_final: 0.6173 (p) REVERT: F 232 ARG cc_start: 0.8457 (mtt180) cc_final: 0.8177 (ptm-80) REVERT: F 244 THR cc_start: 0.6402 (m) cc_final: 0.6109 (m) REVERT: F 312 MET cc_start: 0.6542 (tpp) cc_final: 0.5845 (mmm) REVERT: F 365 PRO cc_start: 0.8019 (Cg_endo) cc_final: 0.7673 (Cg_exo) REVERT: F 433 GLU cc_start: 0.6266 (pt0) cc_final: 0.5896 (mt-10) REVERT: F 461 ILE cc_start: 0.3277 (OUTLIER) cc_final: 0.2646 (pt) REVERT: F 463 ARG cc_start: 0.2380 (OUTLIER) cc_final: 0.1961 (mtp85) REVERT: F 503 LEU cc_start: 0.4888 (OUTLIER) cc_final: 0.4551 (mt) REVERT: F 530 MET cc_start: 0.3772 (mtm) cc_final: 0.3548 (mtt) REVERT: F 535 LYS cc_start: 0.7536 (ttmt) cc_final: 0.7331 (tttp) REVERT: F 553 LEU cc_start: 0.7386 (mt) cc_final: 0.7155 (mp) REVERT: G 160 ASP cc_start: 0.6146 (t70) cc_final: 0.5686 (m-30) REVERT: G 215 VAL cc_start: 0.6304 (OUTLIER) cc_final: 0.6000 (p) REVERT: G 232 ARG cc_start: 0.8489 (mtt180) cc_final: 0.8234 (mtm110) REVERT: G 241 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: G 246 VAL cc_start: 0.6866 (t) cc_final: 0.6475 (p) REVERT: G 255 LYS cc_start: 0.6839 (tttt) cc_final: 0.6551 (tppt) REVERT: G 365 PRO cc_start: 0.7539 (Cg_endo) cc_final: 0.7238 (Cg_exo) REVERT: G 433 GLU cc_start: 0.6087 (pt0) cc_final: 0.5763 (mt-10) REVERT: G 461 ILE cc_start: 0.3359 (OUTLIER) cc_final: 0.3068 (pt) REVERT: G 463 ARG cc_start: 0.1653 (OUTLIER) cc_final: 0.1412 (mtp85) REVERT: G 535 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7561 (tttp) REVERT: G 550 LEU cc_start: 0.7057 (mt) cc_final: 0.6780 (mt) REVERT: G 562 SER cc_start: 0.6525 (m) cc_final: 0.6267 (t) REVERT: G 579 ASN cc_start: 0.6898 (m-40) cc_final: 0.6368 (p0) REVERT: G 591 LEU cc_start: 0.8086 (tp) cc_final: 0.7803 (tp) REVERT: H 167 VAL cc_start: 0.6822 (t) cc_final: 0.5424 (t) REVERT: H 215 VAL cc_start: 0.7648 (OUTLIER) cc_final: 0.7363 (p) REVERT: H 227 ILE cc_start: 0.7517 (mt) cc_final: 0.7175 (mm) REVERT: H 230 MET cc_start: 0.7314 (mtp) cc_final: 0.7102 (tmm) REVERT: H 255 LYS cc_start: 0.6555 (tttt) cc_final: 0.6343 (tppt) REVERT: H 316 GLU cc_start: 0.7936 (tt0) cc_final: 0.7455 (tm-30) REVERT: H 325 ARG cc_start: 0.6595 (ttt180) cc_final: 0.6372 (ttt-90) REVERT: H 345 ASN cc_start: 0.7034 (p0) cc_final: 0.6742 (p0) REVERT: H 407 MET cc_start: 0.5008 (ttp) cc_final: 0.4681 (tmm) REVERT: H 413 SER cc_start: 0.5764 (m) cc_final: 0.5407 (p) REVERT: H 433 GLU cc_start: 0.6432 (pt0) cc_final: 0.6066 (mt-10) REVERT: H 461 ILE cc_start: 0.2519 (OUTLIER) cc_final: 0.1907 (pt) REVERT: H 509 THR cc_start: 0.4432 (p) cc_final: 0.4186 (p) REVERT: H 530 MET cc_start: 0.4488 (mtm) cc_final: 0.4226 (mtt) REVERT: H 535 LYS cc_start: 0.7667 (ttmt) cc_final: 0.7358 (tttp) REVERT: H 550 LEU cc_start: 0.7448 (mt) cc_final: 0.7078 (tt) REVERT: H 562 SER cc_start: 0.6484 (m) cc_final: 0.6134 (t) REVERT: H 567 MET cc_start: 0.4725 (mmm) cc_final: 0.4348 (mmt) REVERT: H 579 ASN cc_start: 0.7262 (m-40) cc_final: 0.6751 (p0) REVERT: I 180 MET cc_start: 0.5274 (mmm) cc_final: 0.5024 (mmp) REVERT: I 183 LEU cc_start: 0.6531 (mt) cc_final: 0.6275 (mt) REVERT: I 249 LEU cc_start: 0.5364 (mt) cc_final: 0.4381 (mp) REVERT: I 298 GLU cc_start: 0.7114 (tt0) cc_final: 0.6774 (pt0) REVERT: I 345 ASN cc_start: 0.6918 (p0) cc_final: 0.6691 (t0) REVERT: I 433 GLU cc_start: 0.6445 (pt0) cc_final: 0.6127 (mt-10) REVERT: I 463 ARG cc_start: 0.2832 (OUTLIER) cc_final: 0.2521 (mmm160) REVERT: I 478 GLU cc_start: 0.7549 (tp30) cc_final: 0.7241 (pp20) REVERT: I 480 ASP cc_start: 0.5224 (OUTLIER) cc_final: 0.5010 (p0) REVERT: I 534 THR cc_start: 0.7569 (m) cc_final: 0.7336 (m) REVERT: I 562 SER cc_start: 0.6426 (m) cc_final: 0.6132 (t) REVERT: J 180 MET cc_start: 0.4405 (mmm) cc_final: 0.4187 (mmm) REVERT: J 229 GLN cc_start: 0.7156 (mt0) cc_final: 0.6785 (mm-40) REVERT: J 236 ARG cc_start: 0.8274 (mtm180) cc_final: 0.7992 (mmm160) REVERT: J 259 GLU cc_start: 0.5913 (mm-30) cc_final: 0.5404 (mt-10) REVERT: J 326 ARG cc_start: 0.4557 (mtm-85) cc_final: 0.4311 (mtm110) REVERT: J 345 ASN cc_start: 0.7023 (p0) cc_final: 0.6607 (t0) REVERT: J 413 SER cc_start: 0.5659 (m) cc_final: 0.5153 (t) REVERT: J 424 PRO cc_start: 0.7689 (Cg_endo) cc_final: 0.7414 (Cg_exo) REVERT: J 433 GLU cc_start: 0.6775 (pt0) cc_final: 0.6439 (mt-10) REVERT: J 461 ILE cc_start: 0.2793 (OUTLIER) cc_final: 0.2220 (pt) REVERT: J 463 ARG cc_start: 0.2679 (OUTLIER) cc_final: 0.2436 (mtp85) REVERT: J 478 GLU cc_start: 0.7706 (tp30) cc_final: 0.7266 (pp20) REVERT: J 503 LEU cc_start: 0.4663 (OUTLIER) cc_final: 0.4320 (mt) REVERT: J 550 LEU cc_start: 0.7299 (mt) cc_final: 0.6907 (tt) REVERT: J 562 SER cc_start: 0.6789 (m) cc_final: 0.6300 (t) REVERT: J 579 ASN cc_start: 0.7080 (m-40) cc_final: 0.6569 (p0) REVERT: J 602 GLN cc_start: 0.6679 (mt0) cc_final: 0.6398 (tp40) REVERT: K 168 ASP cc_start: 0.5282 (m-30) cc_final: 0.5066 (p0) REVERT: K 211 ARG cc_start: 0.5337 (mtt180) cc_final: 0.5095 (mtp85) REVERT: K 227 ILE cc_start: 0.7272 (mt) cc_final: 0.6895 (mm) REVERT: K 259 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5883 (mt-10) REVERT: K 312 MET cc_start: 0.7296 (tpp) cc_final: 0.6958 (mmm) REVERT: K 316 GLU cc_start: 0.8078 (tt0) cc_final: 0.7621 (tm-30) REVERT: K 430 ASP cc_start: 0.3201 (p0) cc_final: 0.2840 (p0) REVERT: K 433 GLU cc_start: 0.6683 (pt0) cc_final: 0.6419 (mt-10) REVERT: K 461 ILE cc_start: 0.2511 (OUTLIER) cc_final: 0.2010 (pt) REVERT: K 463 ARG cc_start: 0.2219 (OUTLIER) cc_final: 0.1808 (mtp85) REVERT: K 535 LYS cc_start: 0.7565 (ttmt) cc_final: 0.7304 (tttm) REVERT: K 550 LEU cc_start: 0.7070 (mt) cc_final: 0.6692 (tt) REVERT: K 562 SER cc_start: 0.6848 (m) cc_final: 0.6424 (t) REVERT: K 567 MET cc_start: 0.5183 (mmm) cc_final: 0.4786 (mmm) REVERT: K 579 ASN cc_start: 0.7070 (m-40) cc_final: 0.6594 (p0) REVERT: L 174 TYR cc_start: 0.4523 (m-80) cc_final: 0.4297 (m-80) REVERT: L 229 GLN cc_start: 0.6929 (mt0) cc_final: 0.6610 (mm-40) REVERT: L 312 MET cc_start: 0.7488 (tpp) cc_final: 0.7225 (mmm) REVERT: L 345 ASN cc_start: 0.6745 (p0) cc_final: 0.6417 (t0) REVERT: L 359 GLN cc_start: 0.5251 (tt0) cc_final: 0.4977 (tp40) REVERT: L 413 SER cc_start: 0.5657 (m) cc_final: 0.5201 (t) REVERT: L 433 GLU cc_start: 0.6859 (pt0) cc_final: 0.6619 (mt-10) REVERT: L 461 ILE cc_start: 0.3046 (OUTLIER) cc_final: 0.2558 (pt) REVERT: L 463 ARG cc_start: 0.3109 (OUTLIER) cc_final: 0.2684 (mtp85) REVERT: L 478 GLU cc_start: 0.7772 (tp30) cc_final: 0.7333 (pp20) REVERT: L 534 THR cc_start: 0.7717 (m) cc_final: 0.7491 (m) REVERT: L 550 LEU cc_start: 0.7405 (mt) cc_final: 0.7025 (tt) REVERT: L 562 SER cc_start: 0.6657 (m) cc_final: 0.6301 (t) REVERT: L 579 ASN cc_start: 0.7154 (m-40) cc_final: 0.6776 (p0) REVERT: L 602 GLN cc_start: 0.6719 (mt0) cc_final: 0.6459 (tp40) REVERT: M 174 TYR cc_start: 0.4053 (m-80) cc_final: 0.3815 (m-80) REVERT: M 229 GLN cc_start: 0.6989 (mt0) cc_final: 0.6706 (mm-40) REVERT: M 325 ARG cc_start: 0.6651 (ttt180) cc_final: 0.6295 (tmt170) REVERT: M 345 ASN cc_start: 0.6900 (p0) cc_final: 0.6606 (t0) REVERT: M 359 GLN cc_start: 0.6013 (tt0) cc_final: 0.5623 (tp40) REVERT: M 413 SER cc_start: 0.5078 (m) cc_final: 0.4595 (t) REVERT: M 430 ASP cc_start: 0.3483 (p0) cc_final: 0.3174 (p0) REVERT: M 433 GLU cc_start: 0.6542 (pt0) cc_final: 0.6191 (mt-10) REVERT: M 461 ILE cc_start: 0.2910 (OUTLIER) cc_final: 0.2498 (pt) REVERT: M 463 ARG cc_start: 0.3010 (OUTLIER) cc_final: 0.2504 (mtp85) REVERT: M 475 GLN cc_start: 0.4524 (tt0) cc_final: 0.4267 (tm-30) REVERT: M 478 GLU cc_start: 0.7667 (tp30) cc_final: 0.7227 (pp20) REVERT: M 550 LEU cc_start: 0.7261 (mt) cc_final: 0.6846 (tt) REVERT: M 562 SER cc_start: 0.6636 (m) cc_final: 0.6264 (t) REVERT: M 579 ASN cc_start: 0.6789 (m-40) cc_final: 0.6272 (p0) REVERT: M 602 GLN cc_start: 0.6639 (mt0) cc_final: 0.6398 (tp40) REVERT: M 613 VAL cc_start: 0.4758 (p) cc_final: 0.4542 (t) REVERT: N 227 ILE cc_start: 0.7457 (mt) cc_final: 0.7206 (mm) REVERT: N 229 GLN cc_start: 0.6994 (mt0) cc_final: 0.6661 (mm-40) REVERT: N 259 GLU cc_start: 0.5829 (mm-30) cc_final: 0.5528 (mt-10) REVERT: N 312 MET cc_start: 0.7468 (tpp) cc_final: 0.7090 (mmm) REVERT: N 345 ASN cc_start: 0.6314 (p0) cc_final: 0.5954 (t0) REVERT: N 359 GLN cc_start: 0.5930 (tt0) cc_final: 0.5524 (tp40) REVERT: N 407 MET cc_start: 0.4538 (ttp) cc_final: 0.4026 (tmm) REVERT: N 413 SER cc_start: 0.5514 (m) cc_final: 0.5042 (t) REVERT: N 424 PRO cc_start: 0.7646 (Cg_endo) cc_final: 0.7347 (Cg_exo) REVERT: N 433 GLU cc_start: 0.6114 (pt0) cc_final: 0.5806 (mt-10) REVERT: N 461 ILE cc_start: 0.2520 (OUTLIER) cc_final: 0.1944 (pt) REVERT: N 463 ARG cc_start: 0.2526 (OUTLIER) cc_final: 0.2231 (mtp85) REVERT: N 478 GLU cc_start: 0.7427 (tp30) cc_final: 0.7062 (pp20) REVERT: N 550 LEU cc_start: 0.7259 (mt) cc_final: 0.6838 (tt) REVERT: N 553 LEU cc_start: 0.7418 (mt) cc_final: 0.7206 (mt) REVERT: N 562 SER cc_start: 0.6543 (m) cc_final: 0.5930 (t) REVERT: N 579 ASN cc_start: 0.6941 (m-40) cc_final: 0.6415 (p0) REVERT: O 167 VAL cc_start: 0.6953 (t) cc_final: 0.6442 (t) REVERT: O 174 TYR cc_start: 0.4429 (m-80) cc_final: 0.4172 (m-80) REVERT: O 227 ILE cc_start: 0.7338 (mt) cc_final: 0.7130 (mm) REVERT: O 259 GLU cc_start: 0.5966 (mm-30) cc_final: 0.5514 (mt-10) REVERT: O 298 GLU cc_start: 0.5711 (tt0) cc_final: 0.5471 (mt-10) REVERT: O 312 MET cc_start: 0.7650 (tpp) cc_final: 0.7320 (mmm) REVERT: O 413 SER cc_start: 0.5145 (m) cc_final: 0.4690 (t) REVERT: O 430 ASP cc_start: 0.3187 (p0) cc_final: 0.2769 (p0) REVERT: O 433 GLU cc_start: 0.6340 (pt0) cc_final: 0.6031 (mt-10) REVERT: O 463 ARG cc_start: 0.2364 (OUTLIER) cc_final: 0.2004 (mtp85) REVERT: O 478 GLU cc_start: 0.7568 (tp30) cc_final: 0.7188 (pp20) REVERT: O 534 THR cc_start: 0.7487 (m) cc_final: 0.7279 (m) REVERT: O 535 LYS cc_start: 0.7640 (ttmt) cc_final: 0.7426 (tttp) REVERT: O 550 LEU cc_start: 0.7099 (mt) cc_final: 0.6578 (tt) REVERT: O 554 PHE cc_start: 0.7057 (m-80) cc_final: 0.6852 (m-80) REVERT: O 562 SER cc_start: 0.6826 (m) cc_final: 0.6391 (t) REVERT: O 579 ASN cc_start: 0.7201 (m-40) cc_final: 0.6753 (p0) REVERT: O 591 LEU cc_start: 0.8327 (tp) cc_final: 0.8062 (tp) REVERT: O 602 GLN cc_start: 0.7117 (mt0) cc_final: 0.6903 (tp-100) outliers start: 263 outliers final: 71 residues processed: 1752 average time/residue: 0.5585 time to fit residues: 1594.0299 Evaluate side-chains 932 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 827 time to evaluate : 4.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 349 GLN Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 241 GLN Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 463 ARG Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 492 SER Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 482 VAL Chi-restraints excluded: chain H residue 492 SER Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain I residue 305 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 463 ARG Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain I residue 482 VAL Chi-restraints excluded: chain I residue 492 SER Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 420 ILE Chi-restraints excluded: chain J residue 461 ILE Chi-restraints excluded: chain J residue 463 ARG Chi-restraints excluded: chain J residue 482 VAL Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 503 LEU Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 420 ILE Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 463 ARG Chi-restraints excluded: chain K residue 482 VAL Chi-restraints excluded: chain K residue 492 SER Chi-restraints excluded: chain K residue 503 LEU Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 463 ARG Chi-restraints excluded: chain L residue 482 VAL Chi-restraints excluded: chain L residue 492 SER Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 593 ARG Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain M residue 305 ILE Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain M residue 461 ILE Chi-restraints excluded: chain M residue 463 ARG Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 492 SER Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain N residue 190 ASP Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 420 ILE Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 463 ARG Chi-restraints excluded: chain N residue 482 VAL Chi-restraints excluded: chain N residue 492 SER Chi-restraints excluded: chain N residue 503 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 305 ILE Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 463 ARG Chi-restraints excluded: chain O residue 482 VAL Chi-restraints excluded: chain O residue 492 SER Chi-restraints excluded: chain O residue 503 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 607 optimal weight: 0.9990 chunk 545 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 368 optimal weight: 0.9980 chunk 291 optimal weight: 4.9990 chunk 564 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 343 optimal weight: 0.7980 chunk 420 optimal weight: 5.9990 chunk 653 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 188 ASN A 328 GLN A 440 GLN A 496 GLN ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 328 GLN B 440 GLN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN ** B 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 328 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 ASN C 440 GLN C 496 GLN C 533 GLN ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN D 440 GLN D 496 GLN E 186 ASN E 328 GLN E 440 GLN E 496 GLN E 533 GLN F 109 ASN F 186 ASN F 188 ASN F 328 GLN F 475 GLN G 186 ASN G 233 GLN G 328 GLN G 440 GLN G 496 GLN ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 188 ASN H 328 GLN H 440 GLN H 496 GLN ** H 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 ASN I 186 ASN I 188 ASN I 328 GLN I 440 GLN I 496 GLN J 109 ASN J 328 GLN J 440 GLN ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 496 GLN K 328 GLN K 394 ASN K 440 GLN ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 GLN L 186 ASN L 188 ASN L 233 GLN L 328 GLN L 349 GLN L 440 GLN L 496 GLN M 186 ASN M 328 GLN M 349 GLN M 440 GLN M 496 GLN N 328 GLN ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 440 GLN N 496 GLN O 186 ASN O 188 ASN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 328 GLN O 345 ASN O 349 GLN O 440 GLN O 496 GLN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3252 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 55485 Z= 0.261 Angle : 0.823 11.257 75255 Z= 0.424 Chirality : 0.052 0.661 9120 Planarity : 0.006 0.119 9855 Dihedral : 8.574 59.657 7990 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.69 % Favored : 95.93 % Rotamer: Outliers : 5.03 % Allowed : 14.21 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -2.25 (0.09), residues: 7200 helix: -0.85 (0.10), residues: 1950 sheet: -1.34 (0.09), residues: 2655 loop : -1.93 (0.10), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 350 HIS 0.007 0.003 HIS K 133 PHE 0.017 0.002 PHE I 393 TYR 0.035 0.003 TYR H 134 ARG 0.010 0.001 ARG M 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 999 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: -0.1076 (ttt) cc_final: -0.1747 (mmt) REVERT: A 259 GLU cc_start: 0.6349 (mm-30) cc_final: 0.5976 (mt-10) REVERT: A 345 ASN cc_start: 0.6278 (p0) cc_final: 0.5657 (t0) REVERT: A 365 PRO cc_start: 0.7512 (Cg_endo) cc_final: 0.7078 (Cg_exo) REVERT: A 407 MET cc_start: 0.3616 (ttp) cc_final: 0.3317 (tmm) REVERT: A 433 GLU cc_start: 0.6827 (pt0) cc_final: 0.6324 (mp0) REVERT: A 478 GLU cc_start: 0.7456 (tp30) cc_final: 0.6774 (pp20) REVERT: A 512 VAL cc_start: 0.3362 (OUTLIER) cc_final: 0.3099 (p) REVERT: B 100 MET cc_start: -0.1022 (ttt) cc_final: -0.1789 (mmt) REVERT: B 180 MET cc_start: 0.6720 (mmt) cc_final: 0.6189 (mmm) REVERT: B 211 ARG cc_start: 0.5938 (mtt180) cc_final: 0.5472 (ptm160) REVERT: B 345 ASN cc_start: 0.6317 (p0) cc_final: 0.5890 (t0) REVERT: B 433 GLU cc_start: 0.6617 (pt0) cc_final: 0.6070 (mp0) REVERT: B 478 GLU cc_start: 0.7226 (tp30) cc_final: 0.6636 (pp20) REVERT: B 536 GLU cc_start: 0.5956 (tm-30) cc_final: 0.5380 (mp0) REVERT: B 550 LEU cc_start: 0.7031 (mt) cc_final: 0.6782 (tt) REVERT: B 579 ASN cc_start: 0.7405 (m-40) cc_final: 0.7069 (p0) REVERT: B 602 GLN cc_start: 0.6901 (mt0) cc_final: 0.6647 (tp40) REVERT: C 209 ASP cc_start: 0.3183 (t0) cc_final: 0.2909 (t0) REVERT: C 211 ARG cc_start: 0.5736 (ttt180) cc_final: 0.5247 (ptm160) REVERT: C 298 GLU cc_start: 0.6015 (mm-30) cc_final: 0.5687 (mt-10) REVERT: C 345 ASN cc_start: 0.6582 (p0) cc_final: 0.6228 (t0) REVERT: C 365 PRO cc_start: 0.7504 (Cg_endo) cc_final: 0.7090 (Cg_exo) REVERT: C 429 MET cc_start: 0.5587 (mmm) cc_final: 0.5232 (mmm) REVERT: C 433 GLU cc_start: 0.6801 (pt0) cc_final: 0.6519 (tt0) REVERT: C 550 LEU cc_start: 0.7141 (mt) cc_final: 0.6816 (tp) REVERT: C 554 PHE cc_start: 0.6303 (m-80) cc_final: 0.6026 (m-80) REVERT: C 579 ASN cc_start: 0.7511 (m-40) cc_final: 0.7106 (p0) REVERT: D 179 GLU cc_start: 0.5298 (tm-30) cc_final: 0.4725 (tm-30) REVERT: D 245 ARG cc_start: 0.4501 (ttt180) cc_final: 0.4294 (mtp85) REVERT: D 345 ASN cc_start: 0.6658 (p0) cc_final: 0.6397 (t0) REVERT: D 365 PRO cc_start: 0.7358 (Cg_endo) cc_final: 0.7040 (Cg_exo) REVERT: D 433 GLU cc_start: 0.6609 (pt0) cc_final: 0.6349 (tt0) REVERT: D 463 ARG cc_start: 0.2572 (OUTLIER) cc_final: 0.2309 (mtp85) REVERT: D 550 LEU cc_start: 0.6570 (mt) cc_final: 0.6212 (tp) REVERT: D 554 PHE cc_start: 0.6779 (m-80) cc_final: 0.6484 (m-80) REVERT: E 180 MET cc_start: 0.6934 (mmm) cc_final: 0.6410 (mmm) REVERT: E 359 GLN cc_start: 0.5202 (tt0) cc_final: 0.4783 (tp40) REVERT: E 433 GLU cc_start: 0.6052 (pt0) cc_final: 0.5746 (mt-10) REVERT: E 478 GLU cc_start: 0.7058 (tp30) cc_final: 0.6572 (pp20) REVERT: F 100 MET cc_start: 0.2397 (mmm) cc_final: 0.2186 (mmm) REVERT: F 312 MET cc_start: 0.6855 (tpp) cc_final: 0.6351 (mmm) REVERT: F 433 GLU cc_start: 0.7037 (pt0) cc_final: 0.6740 (tt0) REVERT: F 536 GLU cc_start: 0.6612 (tm-30) cc_final: 0.6135 (tm-30) REVERT: G 215 VAL cc_start: 0.6688 (OUTLIER) cc_final: 0.6468 (p) REVERT: G 230 MET cc_start: 0.6386 (mmp) cc_final: 0.6160 (tmm) REVERT: G 433 GLU cc_start: 0.6937 (pt0) cc_final: 0.6561 (mt-10) REVERT: G 461 ILE cc_start: 0.2326 (OUTLIER) cc_final: 0.2044 (pt) REVERT: G 550 LEU cc_start: 0.6859 (mt) cc_final: 0.6574 (tp) REVERT: H 160 ASP cc_start: 0.3324 (t70) cc_final: 0.2715 (m-30) REVERT: H 207 VAL cc_start: 0.0895 (OUTLIER) cc_final: 0.0578 (t) REVERT: H 224 ARG cc_start: 0.5619 (mtt180) cc_final: 0.5329 (mtt-85) REVERT: H 227 ILE cc_start: 0.7529 (mt) cc_final: 0.7304 (mm) REVERT: H 316 GLU cc_start: 0.7785 (tt0) cc_final: 0.7354 (tm-30) REVERT: H 365 PRO cc_start: 0.7599 (Cg_endo) cc_final: 0.7328 (Cg_exo) REVERT: H 433 GLU cc_start: 0.6852 (pt0) cc_final: 0.6477 (mt-10) REVERT: H 461 ILE cc_start: 0.2883 (OUTLIER) cc_final: 0.2673 (pt) REVERT: I 433 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6342 (tt0) REVERT: I 463 ARG cc_start: 0.2948 (OUTLIER) cc_final: 0.2579 (mmt-90) REVERT: I 478 GLU cc_start: 0.7455 (tp30) cc_final: 0.6952 (pt0) REVERT: I 480 ASP cc_start: 0.5386 (OUTLIER) cc_final: 0.5124 (p0) REVERT: I 557 THR cc_start: 0.5850 (m) cc_final: 0.5086 (m) REVERT: J 172 LEU cc_start: 0.3396 (mt) cc_final: 0.3078 (tp) REVERT: J 174 TYR cc_start: 0.3110 (m-80) cc_final: 0.2580 (m-80) REVERT: J 209 ASP cc_start: 0.3433 (t0) cc_final: 0.3017 (t0) REVERT: J 326 ARG cc_start: 0.4820 (mtm-85) cc_final: 0.4279 (mtm110) REVERT: J 345 ASN cc_start: 0.6627 (p0) cc_final: 0.6331 (t0) REVERT: J 359 GLN cc_start: 0.5811 (tt0) cc_final: 0.5154 (tp40) REVERT: J 423 THR cc_start: 0.6349 (OUTLIER) cc_final: 0.6149 (p) REVERT: J 433 GLU cc_start: 0.6828 (pt0) cc_final: 0.6365 (mp0) REVERT: J 461 ILE cc_start: 0.2828 (OUTLIER) cc_final: 0.2521 (pt) REVERT: J 478 GLU cc_start: 0.7459 (tp30) cc_final: 0.6711 (pp20) REVERT: J 536 GLU cc_start: 0.6247 (tm-30) cc_final: 0.5840 (mp0) REVERT: J 550 LEU cc_start: 0.6869 (mt) cc_final: 0.6623 (tp) REVERT: J 554 PHE cc_start: 0.6816 (m-80) cc_final: 0.6554 (m-80) REVERT: J 557 THR cc_start: 0.5700 (m) cc_final: 0.5179 (m) REVERT: J 579 ASN cc_start: 0.7094 (m-40) cc_final: 0.6593 (p0) REVERT: K 312 MET cc_start: 0.7771 (tpp) cc_final: 0.7554 (mmm) REVERT: K 316 GLU cc_start: 0.7837 (tt0) cc_final: 0.7381 (tm-30) REVERT: K 365 PRO cc_start: 0.7243 (Cg_endo) cc_final: 0.6753 (Cg_exo) REVERT: K 433 GLU cc_start: 0.6633 (pt0) cc_final: 0.6215 (mp0) REVERT: K 534 THR cc_start: 0.7052 (m) cc_final: 0.6539 (m) REVERT: K 536 GLU cc_start: 0.6605 (tm-30) cc_final: 0.6228 (mp0) REVERT: K 550 LEU cc_start: 0.6785 (mt) cc_final: 0.6459 (tp) REVERT: K 567 MET cc_start: 0.5249 (mmm) cc_final: 0.4998 (mmm) REVERT: L 207 VAL cc_start: 0.2996 (OUTLIER) cc_final: 0.2647 (t) REVERT: L 345 ASN cc_start: 0.6473 (p0) cc_final: 0.6233 (t0) REVERT: L 407 MET cc_start: 0.2722 (tmm) cc_final: 0.2491 (tmm) REVERT: L 429 MET cc_start: 0.5313 (mmm) cc_final: 0.4982 (mmm) REVERT: L 433 GLU cc_start: 0.6824 (pt0) cc_final: 0.6396 (mp0) REVERT: L 463 ARG cc_start: 0.2679 (OUTLIER) cc_final: 0.2258 (mtp85) REVERT: L 478 GLU cc_start: 0.7762 (tp30) cc_final: 0.7214 (pp20) REVERT: L 534 THR cc_start: 0.7103 (m) cc_final: 0.6688 (m) REVERT: L 536 GLU cc_start: 0.6334 (tm-30) cc_final: 0.5759 (mp0) REVERT: L 579 ASN cc_start: 0.6874 (m-40) cc_final: 0.6508 (p0) REVERT: M 174 TYR cc_start: 0.3886 (m-80) cc_final: 0.3372 (m-80) REVERT: M 345 ASN cc_start: 0.6567 (p0) cc_final: 0.6273 (t0) REVERT: M 359 GLN cc_start: 0.5718 (tt0) cc_final: 0.5151 (tp40) REVERT: M 429 MET cc_start: 0.5053 (mmm) cc_final: 0.4570 (mmm) REVERT: M 433 GLU cc_start: 0.6467 (pt0) cc_final: 0.5972 (mp0) REVERT: M 478 GLU cc_start: 0.7500 (tp30) cc_final: 0.6992 (pp20) REVERT: M 550 LEU cc_start: 0.6985 (mt) cc_final: 0.6677 (tp) REVERT: M 579 ASN cc_start: 0.6945 (m-40) cc_final: 0.6495 (p0) REVERT: N 211 ARG cc_start: 0.5812 (mtt180) cc_final: 0.5238 (ptm-80) REVERT: N 298 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5826 (mt-10) REVERT: N 312 MET cc_start: 0.7445 (tpp) cc_final: 0.7242 (mmm) REVERT: N 345 ASN cc_start: 0.6140 (p0) cc_final: 0.5655 (t0) REVERT: N 365 PRO cc_start: 0.7158 (Cg_endo) cc_final: 0.6784 (Cg_exo) REVERT: N 407 MET cc_start: 0.3904 (ttp) cc_final: 0.3270 (tmm) REVERT: N 478 GLU cc_start: 0.7439 (tp30) cc_final: 0.6984 (pp20) REVERT: N 579 ASN cc_start: 0.6882 (m-40) cc_final: 0.6551 (p0) REVERT: O 172 LEU cc_start: 0.3357 (OUTLIER) cc_final: 0.2946 (mt) REVERT: O 179 GLU cc_start: 0.4484 (tm-30) cc_final: 0.4271 (tm-30) REVERT: O 207 VAL cc_start: 0.1247 (OUTLIER) cc_final: 0.0894 (t) REVERT: O 211 ARG cc_start: 0.5337 (mtp85) cc_final: 0.5060 (ptm160) REVERT: O 259 GLU cc_start: 0.6264 (mm-30) cc_final: 0.5947 (mt-10) REVERT: O 312 MET cc_start: 0.7851 (tpp) cc_final: 0.7631 (mmm) REVERT: O 365 PRO cc_start: 0.7088 (Cg_endo) cc_final: 0.6685 (Cg_exo) REVERT: O 407 MET cc_start: 0.3844 (OUTLIER) cc_final: 0.3299 (tmm) REVERT: O 433 GLU cc_start: 0.6324 (pt0) cc_final: 0.5961 (mp0) REVERT: O 478 GLU cc_start: 0.7357 (tp30) cc_final: 0.6850 (pp20) REVERT: O 534 THR cc_start: 0.7361 (m) cc_final: 0.7160 (m) REVERT: O 536 GLU cc_start: 0.6582 (tm-30) cc_final: 0.6025 (mp0) REVERT: O 550 LEU cc_start: 0.6978 (mt) cc_final: 0.6688 (tt) REVERT: O 553 LEU cc_start: 0.7558 (mt) cc_final: 0.7065 (tp) REVERT: O 579 ASN cc_start: 0.7161 (m-40) cc_final: 0.6744 (p0) outliers start: 304 outliers final: 118 residues processed: 1238 average time/residue: 0.5205 time to fit residues: 1106.0597 Evaluate side-chains 852 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 718 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 350 TRP Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 559 ASN Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 349 GLN Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 559 ASN Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 463 ARG Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 298 GLU Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 461 ILE Chi-restraints excluded: chain J residue 465 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 559 ASN Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 530 MET Chi-restraints excluded: chain K residue 559 ASN Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 463 ARG Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 559 ASN Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 465 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 530 MET Chi-restraints excluded: chain M residue 559 ASN Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 190 ASP Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 530 MET Chi-restraints excluded: chain N residue 559 ASN Chi-restraints excluded: chain O residue 172 LEU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 207 VAL Chi-restraints excluded: chain O residue 258 VAL Chi-restraints excluded: chain O residue 407 MET Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 465 THR Chi-restraints excluded: chain O residue 482 VAL Chi-restraints excluded: chain O residue 559 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 363 optimal weight: 30.0000 chunk 202 optimal weight: 10.0000 chunk 544 optimal weight: 9.9990 chunk 445 optimal weight: 0.3980 chunk 180 optimal weight: 7.9990 chunk 655 optimal weight: 6.9990 chunk 707 optimal weight: 1.9990 chunk 583 optimal weight: 20.0000 chunk 649 optimal weight: 9.9990 chunk 223 optimal weight: 0.0040 chunk 525 optimal weight: 5.9990 overall best weight: 3.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN B 475 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 ASN ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN E 533 GLN F 440 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 496 GLN G 533 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 533 GLN ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 392 ASN ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN M 533 GLN M 595 GLN ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 GLN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3272 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 55485 Z= 0.317 Angle : 0.787 10.583 75255 Z= 0.403 Chirality : 0.049 0.218 9120 Planarity : 0.006 0.103 9855 Dihedral : 6.851 59.161 7838 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.68 % Favored : 94.90 % Rotamer: Outliers : 4.53 % Allowed : 18.61 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -2.18 (0.09), residues: 7200 helix: -0.31 (0.11), residues: 1950 sheet: -1.69 (0.09), residues: 2595 loop : -1.82 (0.11), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 350 HIS 0.005 0.002 HIS D 133 PHE 0.019 0.002 PHE J 592 TYR 0.039 0.003 TYR K 134 ARG 0.011 0.001 ARG I 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 848 time to evaluate : 4.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ILE cc_start: 0.7196 (mm) cc_final: 0.6689 (tp) REVERT: A 259 GLU cc_start: 0.6274 (mm-30) cc_final: 0.6070 (pt0) REVERT: A 365 PRO cc_start: 0.7541 (Cg_endo) cc_final: 0.7172 (Cg_exo) REVERT: A 429 MET cc_start: 0.5750 (mmm) cc_final: 0.5538 (mmm) REVERT: A 433 GLU cc_start: 0.6302 (pt0) cc_final: 0.5880 (mp0) REVERT: A 461 ILE cc_start: 0.3240 (OUTLIER) cc_final: 0.3007 (pt) REVERT: B 211 ARG cc_start: 0.5968 (mtt180) cc_final: 0.5232 (ptm160) REVERT: B 433 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6228 (mp0) REVERT: B 478 GLU cc_start: 0.7314 (tp30) cc_final: 0.6769 (pp20) REVERT: B 536 GLU cc_start: 0.5464 (tm-30) cc_final: 0.5073 (mp0) REVERT: B 550 LEU cc_start: 0.6975 (mt) cc_final: 0.6726 (tp) REVERT: B 579 ASN cc_start: 0.7337 (m-40) cc_final: 0.6973 (p0) REVERT: B 602 GLN cc_start: 0.6851 (mt0) cc_final: 0.6578 (tp40) REVERT: C 207 VAL cc_start: 0.3010 (OUTLIER) cc_final: 0.2778 (t) REVERT: C 211 ARG cc_start: 0.5716 (ttt180) cc_final: 0.5243 (ptm160) REVERT: C 238 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5530 (tp) REVERT: C 297 ASP cc_start: 0.4935 (t0) cc_final: 0.4059 (t0) REVERT: C 298 GLU cc_start: 0.5979 (mm-30) cc_final: 0.5611 (mt-10) REVERT: C 365 PRO cc_start: 0.7477 (Cg_endo) cc_final: 0.7149 (Cg_exo) REVERT: C 433 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6567 (tt0) REVERT: C 550 LEU cc_start: 0.7310 (mt) cc_final: 0.7069 (tp) REVERT: C 554 PHE cc_start: 0.6179 (m-80) cc_final: 0.5946 (m-80) REVERT: D 209 ASP cc_start: 0.3752 (t0) cc_final: 0.3537 (t0) REVERT: D 211 ARG cc_start: 0.4822 (mtt180) cc_final: 0.4557 (ptm160) REVERT: D 365 PRO cc_start: 0.7417 (Cg_endo) cc_final: 0.7121 (Cg_exo) REVERT: D 433 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6435 (tt0) REVERT: E 174 TYR cc_start: 0.3232 (m-80) cc_final: 0.2960 (m-80) REVERT: E 179 GLU cc_start: 0.5000 (tm-30) cc_final: 0.4610 (tm-30) REVERT: E 336 VAL cc_start: 0.5717 (OUTLIER) cc_final: 0.5390 (m) REVERT: E 407 MET cc_start: 0.2707 (tmm) cc_final: 0.2397 (tmm) REVERT: E 433 GLU cc_start: 0.5775 (pt0) cc_final: 0.5460 (mt-10) REVERT: E 478 GLU cc_start: 0.6917 (tp30) cc_final: 0.6498 (pp20) REVERT: F 160 ASP cc_start: 0.6136 (t70) cc_final: 0.5677 (m-30) REVERT: F 180 MET cc_start: 0.6821 (mmm) cc_final: 0.6394 (mmm) REVERT: F 207 VAL cc_start: 0.1002 (OUTLIER) cc_final: 0.0582 (t) REVERT: F 312 MET cc_start: 0.6830 (tpp) cc_final: 0.6339 (mmm) REVERT: F 433 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6848 (tt0) REVERT: G 433 GLU cc_start: 0.7121 (pt0) cc_final: 0.6788 (mt-10) REVERT: H 316 GLU cc_start: 0.7984 (tt0) cc_final: 0.7569 (tm-30) REVERT: H 407 MET cc_start: 0.4659 (tmm) cc_final: 0.4409 (tmm) REVERT: H 433 GLU cc_start: 0.6916 (pt0) cc_final: 0.6548 (mt-10) REVERT: I 407 MET cc_start: 0.2999 (ttt) cc_final: 0.2652 (tpp) REVERT: I 423 THR cc_start: 0.6266 (OUTLIER) cc_final: 0.5960 (p) REVERT: I 433 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6371 (tt0) REVERT: I 463 ARG cc_start: 0.2929 (OUTLIER) cc_final: 0.2465 (mmt180) REVERT: I 480 ASP cc_start: 0.6001 (OUTLIER) cc_final: 0.5640 (p0) REVERT: J 172 LEU cc_start: 0.3173 (mt) cc_final: 0.2682 (tp) REVERT: J 238 LEU cc_start: 0.5351 (OUTLIER) cc_final: 0.5043 (tp) REVERT: J 407 MET cc_start: 0.2392 (tmm) cc_final: 0.1915 (tmm) REVERT: J 431 ASN cc_start: 0.6007 (m-40) cc_final: 0.5759 (m-40) REVERT: J 433 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6521 (mt-10) REVERT: J 536 GLU cc_start: 0.6276 (tm-30) cc_final: 0.5865 (mp0) REVERT: J 550 LEU cc_start: 0.6890 (mt) cc_final: 0.6608 (tp) REVERT: J 598 ASP cc_start: 0.7555 (m-30) cc_final: 0.7319 (p0) REVERT: K 312 MET cc_start: 0.7758 (tpp) cc_final: 0.7427 (mmm) REVERT: K 316 GLU cc_start: 0.7929 (tt0) cc_final: 0.7488 (tm-30) REVERT: K 365 PRO cc_start: 0.7461 (Cg_endo) cc_final: 0.7109 (Cg_exo) REVERT: K 407 MET cc_start: 0.2248 (tmm) cc_final: 0.1980 (tmm) REVERT: K 433 GLU cc_start: 0.6597 (pt0) cc_final: 0.6222 (mp0) REVERT: K 550 LEU cc_start: 0.6505 (mt) cc_final: 0.6234 (tp) REVERT: K 567 MET cc_start: 0.5087 (mmm) cc_final: 0.4864 (mmm) REVERT: L 172 LEU cc_start: 0.3265 (OUTLIER) cc_final: 0.2419 (tt) REVERT: L 207 VAL cc_start: 0.3206 (OUTLIER) cc_final: 0.2752 (t) REVERT: L 216 VAL cc_start: 0.6828 (t) cc_final: 0.6478 (t) REVERT: L 251 TYR cc_start: 0.5873 (m-80) cc_final: 0.5244 (m-80) REVERT: L 326 ARG cc_start: 0.3560 (mtm110) cc_final: 0.3153 (mtp-110) REVERT: L 429 MET cc_start: 0.5668 (mmm) cc_final: 0.5464 (mmm) REVERT: L 431 ASN cc_start: 0.5816 (m-40) cc_final: 0.5555 (m110) REVERT: L 433 GLU cc_start: 0.6885 (pt0) cc_final: 0.6509 (mp0) REVERT: L 478 GLU cc_start: 0.7536 (tp30) cc_final: 0.7000 (pp20) REVERT: L 534 THR cc_start: 0.7339 (m) cc_final: 0.6597 (m) REVERT: L 536 GLU cc_start: 0.6348 (tm-30) cc_final: 0.5788 (mp0) REVERT: L 579 ASN cc_start: 0.7019 (m-40) cc_final: 0.6630 (p0) REVERT: M 174 TYR cc_start: 0.3747 (m-80) cc_final: 0.3430 (m-80) REVERT: M 251 TYR cc_start: 0.5644 (m-80) cc_final: 0.5263 (m-80) REVERT: M 326 ARG cc_start: 0.3304 (mtm110) cc_final: 0.3012 (mtm110) REVERT: M 359 GLN cc_start: 0.5869 (tt0) cc_final: 0.5425 (tp40) REVERT: M 407 MET cc_start: 0.2239 (tmm) cc_final: 0.2012 (tmm) REVERT: M 431 ASN cc_start: 0.6018 (m-40) cc_final: 0.5756 (m110) REVERT: M 433 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6159 (mt-10) REVERT: M 475 GLN cc_start: 0.4117 (tt0) cc_final: 0.3632 (tm-30) REVERT: M 478 GLU cc_start: 0.7506 (tp30) cc_final: 0.6973 (pp20) REVERT: M 579 ASN cc_start: 0.6956 (m-40) cc_final: 0.6464 (p0) REVERT: N 174 TYR cc_start: 0.3107 (m-80) cc_final: 0.2569 (m-80) REVERT: N 211 ARG cc_start: 0.6368 (mtt180) cc_final: 0.5643 (ptm-80) REVERT: N 251 TYR cc_start: 0.6241 (m-80) cc_final: 0.5619 (m-80) REVERT: N 298 GLU cc_start: 0.6533 (mm-30) cc_final: 0.6321 (mt-10) REVERT: N 312 MET cc_start: 0.7844 (tpp) cc_final: 0.7454 (mmm) REVERT: N 359 GLN cc_start: 0.5964 (tt0) cc_final: 0.5756 (tp40) REVERT: N 407 MET cc_start: 0.3968 (ttp) cc_final: 0.3414 (tmm) REVERT: N 433 GLU cc_start: 0.5525 (pp20) cc_final: 0.5164 (tt0) REVERT: O 179 GLU cc_start: 0.4773 (tm-30) cc_final: 0.4404 (tm-30) REVERT: O 211 ARG cc_start: 0.5393 (mtp85) cc_final: 0.5162 (ptt90) REVERT: O 251 TYR cc_start: 0.6018 (m-80) cc_final: 0.5542 (m-80) REVERT: O 259 GLU cc_start: 0.6032 (mm-30) cc_final: 0.5665 (mt-10) REVERT: O 312 MET cc_start: 0.7900 (tpp) cc_final: 0.7608 (mmm) REVERT: O 365 PRO cc_start: 0.7377 (Cg_endo) cc_final: 0.6948 (Cg_exo) REVERT: O 429 MET cc_start: 0.5315 (mmm) cc_final: 0.5067 (mmm) REVERT: O 433 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.5957 (mt-10) REVERT: O 553 LEU cc_start: 0.7311 (mt) cc_final: 0.7092 (tp) REVERT: O 579 ASN cc_start: 0.7086 (m-40) cc_final: 0.6684 (p0) REVERT: O 598 ASP cc_start: 0.7471 (m-30) cc_final: 0.7101 (p0) outliers start: 274 outliers final: 155 residues processed: 1051 average time/residue: 0.5276 time to fit residues: 948.1558 Evaluate side-chains 859 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 685 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 559 ASN Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 557 THR Chi-restraints excluded: chain H residue 559 ASN Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 463 ARG Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 350 TRP Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 465 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 559 ASN Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 336 VAL Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 530 MET Chi-restraints excluded: chain K residue 557 THR Chi-restraints excluded: chain K residue 559 ASN Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain L residue 350 TRP Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 465 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 530 MET Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 337 GLU Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 465 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 512 VAL Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 647 optimal weight: 0.9980 chunk 492 optimal weight: 6.9990 chunk 339 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 312 optimal weight: 0.9980 chunk 439 optimal weight: 1.9990 chunk 657 optimal weight: 1.9990 chunk 695 optimal weight: 0.2980 chunk 343 optimal weight: 4.9990 chunk 623 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 595 GLN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 533 GLN F 109 ASN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN G 138 ASN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN J 533 GLN K 392 ASN ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN L 587 ASN M 233 GLN M 533 GLN ** N 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN O 602 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3272 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 55485 Z= 0.184 Angle : 0.691 11.957 75255 Z= 0.347 Chirality : 0.047 0.244 9120 Planarity : 0.005 0.088 9855 Dihedral : 5.944 58.585 7802 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.22 % Favored : 96.36 % Rotamer: Outliers : 3.80 % Allowed : 20.55 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -1.80 (0.09), residues: 7200 helix: 0.17 (0.11), residues: 1950 sheet: -1.33 (0.10), residues: 2445 loop : -1.91 (0.11), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 350 HIS 0.006 0.002 HIS K 133 PHE 0.011 0.001 PHE I 592 TYR 0.029 0.002 TYR I 552 ARG 0.011 0.000 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 810 time to evaluate : 4.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4760 (tp) REVERT: A 300 THR cc_start: 0.6983 (OUTLIER) cc_final: 0.6664 (p) REVERT: A 365 PRO cc_start: 0.7427 (Cg_endo) cc_final: 0.7036 (Cg_exo) REVERT: A 407 MET cc_start: 0.3109 (ttp) cc_final: 0.2539 (tmm) REVERT: A 433 GLU cc_start: 0.6802 (pt0) cc_final: 0.6489 (pp20) REVERT: B 209 ASP cc_start: 0.3235 (t0) cc_final: 0.2945 (t0) REVERT: B 211 ARG cc_start: 0.5785 (mtt180) cc_final: 0.5529 (ptm160) REVERT: B 359 GLN cc_start: 0.5778 (tt0) cc_final: 0.5523 (tp40) REVERT: B 433 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6300 (mt-10) REVERT: B 478 GLU cc_start: 0.7314 (tp30) cc_final: 0.6687 (pp20) REVERT: B 536 GLU cc_start: 0.5727 (tm-30) cc_final: 0.5388 (mp0) REVERT: B 550 LEU cc_start: 0.6990 (mt) cc_final: 0.6740 (tp) REVERT: B 602 GLN cc_start: 0.6754 (mt0) cc_final: 0.6522 (tp40) REVERT: C 179 GLU cc_start: 0.5229 (tm-30) cc_final: 0.4983 (tm-30) REVERT: C 211 ARG cc_start: 0.5801 (ttt180) cc_final: 0.5271 (ptm160) REVERT: C 300 THR cc_start: 0.6494 (OUTLIER) cc_final: 0.6190 (p) REVERT: C 365 PRO cc_start: 0.7415 (Cg_endo) cc_final: 0.7108 (Cg_exo) REVERT: C 407 MET cc_start: 0.1439 (tmm) cc_final: 0.1213 (tmm) REVERT: C 433 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6598 (tt0) REVERT: D 179 GLU cc_start: 0.5305 (tm-30) cc_final: 0.4911 (tm-30) REVERT: D 209 ASP cc_start: 0.4120 (t70) cc_final: 0.3686 (t0) REVERT: D 365 PRO cc_start: 0.7367 (Cg_endo) cc_final: 0.7008 (Cg_exo) REVERT: D 423 THR cc_start: 0.5488 (p) cc_final: 0.5234 (t) REVERT: D 433 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6378 (tt0) REVERT: E 174 TYR cc_start: 0.3318 (m-80) cc_final: 0.3040 (m-80) REVERT: E 179 GLU cc_start: 0.5172 (tm-30) cc_final: 0.4777 (tm-30) REVERT: E 180 MET cc_start: 0.5975 (mmm) cc_final: 0.5725 (mpp) REVERT: E 336 VAL cc_start: 0.5710 (OUTLIER) cc_final: 0.5509 (m) REVERT: E 365 PRO cc_start: 0.7602 (Cg_endo) cc_final: 0.7331 (Cg_exo) REVERT: E 433 GLU cc_start: 0.6543 (pt0) cc_final: 0.6181 (mt-10) REVERT: E 478 GLU cc_start: 0.6957 (tp30) cc_final: 0.6550 (pp20) REVERT: E 536 GLU cc_start: 0.6266 (tm-30) cc_final: 0.5929 (mp0) REVERT: F 230 MET cc_start: 0.6835 (mmt) cc_final: 0.6215 (tmm) REVERT: F 312 MET cc_start: 0.7117 (tpp) cc_final: 0.6605 (mmm) REVERT: F 322 LEU cc_start: 0.7073 (tp) cc_final: 0.6832 (mt) REVERT: F 433 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6810 (tt0) REVERT: G 160 ASP cc_start: 0.5971 (t70) cc_final: 0.5632 (m-30) REVERT: G 300 THR cc_start: 0.5602 (OUTLIER) cc_final: 0.5187 (p) REVERT: G 433 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6627 (mt-10) REVERT: G 579 ASN cc_start: 0.6827 (t0) cc_final: 0.6379 (t0) REVERT: H 100 MET cc_start: 0.1362 (ttt) cc_final: 0.0506 (mmm) REVERT: H 316 GLU cc_start: 0.8027 (tt0) cc_final: 0.7636 (tm-30) REVERT: H 322 LEU cc_start: 0.6705 (tp) cc_final: 0.6343 (mt) REVERT: H 433 GLU cc_start: 0.6845 (pt0) cc_final: 0.6455 (mt-10) REVERT: H 536 GLU cc_start: 0.6286 (tm-30) cc_final: 0.5813 (mp0) REVERT: I 433 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6366 (tt0) REVERT: I 480 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.6431 (p0) REVERT: I 589 TYR cc_start: 0.6539 (t80) cc_final: 0.6192 (t80) REVERT: I 591 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8397 (tp) REVERT: J 407 MET cc_start: 0.2106 (tmm) cc_final: 0.1811 (tmm) REVERT: J 433 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6391 (mp0) REVERT: J 536 GLU cc_start: 0.6271 (tm-30) cc_final: 0.5832 (mp0) REVERT: J 550 LEU cc_start: 0.6954 (mt) cc_final: 0.6637 (tp) REVERT: K 300 THR cc_start: 0.6135 (OUTLIER) cc_final: 0.5926 (p) REVERT: K 312 MET cc_start: 0.7576 (tpp) cc_final: 0.7172 (mmm) REVERT: K 316 GLU cc_start: 0.7865 (tt0) cc_final: 0.7452 (tm-30) REVERT: K 407 MET cc_start: 0.2380 (tmm) cc_final: 0.2094 (tmm) REVERT: K 433 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: K 550 LEU cc_start: 0.6976 (mt) cc_final: 0.6689 (tp) REVERT: K 579 ASN cc_start: 0.7024 (t0) cc_final: 0.6553 (t0) REVERT: L 251 TYR cc_start: 0.5914 (m-80) cc_final: 0.5202 (m-80) REVERT: L 407 MET cc_start: 0.2226 (tmm) cc_final: 0.2015 (tmm) REVERT: L 433 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: L 463 ARG cc_start: 0.2734 (OUTLIER) cc_final: 0.2480 (mtp85) REVERT: L 478 GLU cc_start: 0.7566 (tp30) cc_final: 0.7028 (pp20) REVERT: L 534 THR cc_start: 0.7376 (m) cc_final: 0.6677 (m) REVERT: L 536 GLU cc_start: 0.6484 (tm-30) cc_final: 0.5976 (mp0) REVERT: L 579 ASN cc_start: 0.6975 (m-40) cc_final: 0.6668 (t0) REVERT: M 251 TYR cc_start: 0.5827 (m-80) cc_final: 0.5261 (m-80) REVERT: M 300 THR cc_start: 0.6182 (OUTLIER) cc_final: 0.5955 (p) REVERT: M 359 GLN cc_start: 0.5623 (tt0) cc_final: 0.5269 (tp40) REVERT: M 433 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6208 (tt0) REVERT: N 209 ASP cc_start: 0.3344 (t0) cc_final: 0.2751 (t0) REVERT: N 211 ARG cc_start: 0.6324 (mtt180) cc_final: 0.5812 (ptm-80) REVERT: N 251 TYR cc_start: 0.6068 (m-80) cc_final: 0.5580 (m-80) REVERT: N 312 MET cc_start: 0.7787 (tpp) cc_final: 0.7517 (mmm) REVERT: N 359 GLN cc_start: 0.5970 (tt0) cc_final: 0.5708 (tp40) REVERT: N 407 MET cc_start: 0.4390 (ttp) cc_final: 0.3692 (tmm) REVERT: N 433 GLU cc_start: 0.5446 (pp20) cc_final: 0.5077 (tt0) REVERT: N 579 ASN cc_start: 0.7339 (t0) cc_final: 0.6878 (p0) REVERT: O 179 GLU cc_start: 0.4874 (tm-30) cc_final: 0.4520 (tm-30) REVERT: O 211 ARG cc_start: 0.5336 (mtp85) cc_final: 0.5103 (ptm160) REVERT: O 251 TYR cc_start: 0.5897 (m-80) cc_final: 0.5426 (m-80) REVERT: O 259 GLU cc_start: 0.6028 (mm-30) cc_final: 0.5567 (mt-10) REVERT: O 300 THR cc_start: 0.6241 (OUTLIER) cc_final: 0.6004 (p) REVERT: O 312 MET cc_start: 0.7821 (tpp) cc_final: 0.7513 (mmm) REVERT: O 429 MET cc_start: 0.5280 (mmm) cc_final: 0.5029 (mmm) REVERT: O 433 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5933 (mt-10) REVERT: O 478 GLU cc_start: 0.7272 (tp30) cc_final: 0.6848 (pp20) REVERT: O 534 THR cc_start: 0.7016 (m) cc_final: 0.6627 (m) REVERT: O 536 GLU cc_start: 0.6208 (tm-30) cc_final: 0.5605 (mp0) REVERT: O 579 ASN cc_start: 0.7205 (m-40) cc_final: 0.6961 (t0) outliers start: 230 outliers final: 116 residues processed: 979 average time/residue: 0.5127 time to fit residues: 869.7336 Evaluate side-chains 821 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 683 time to evaluate : 4.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 573 THR Chi-restraints excluded: chain H residue 613 VAL Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain I residue 591 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 350 TRP Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 465 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 559 ASN Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 433 GLU Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 463 ARG Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 550 LEU Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 465 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 591 LEU Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 460 THR Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 464 LYS Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 579 optimal weight: 8.9990 chunk 395 optimal weight: 10.0000 chunk 10 optimal weight: 0.0870 chunk 518 optimal weight: 0.7980 chunk 287 optimal weight: 0.8980 chunk 593 optimal weight: 0.9990 chunk 481 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 355 optimal weight: 7.9990 chunk 624 optimal weight: 40.0000 chunk 175 optimal weight: 1.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 533 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN I 301 ASN I 345 ASN J 475 GLN J 533 GLN K 233 GLN K 392 ASN ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN M 188 ASN ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 533 GLN ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 ASN N 233 GLN ** N 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3278 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 55485 Z= 0.191 Angle : 0.670 11.323 75255 Z= 0.337 Chirality : 0.046 0.250 9120 Planarity : 0.005 0.086 9855 Dihedral : 5.675 59.064 7794 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.89 % Favored : 95.69 % Rotamer: Outliers : 4.04 % Allowed : 21.03 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -1.62 (0.09), residues: 7200 helix: 0.36 (0.11), residues: 1950 sheet: -1.27 (0.10), residues: 2445 loop : -1.80 (0.11), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 350 HIS 0.005 0.002 HIS A 133 PHE 0.027 0.002 PHE H 393 TYR 0.034 0.002 TYR B 134 ARG 0.010 0.000 ARG M 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 748 time to evaluate : 4.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: -0.1095 (ttt) cc_final: -0.1757 (mmt) REVERT: A 180 MET cc_start: 0.6597 (mtm) cc_final: 0.6324 (mtt) REVERT: A 238 LEU cc_start: 0.5208 (OUTLIER) cc_final: 0.4776 (tp) REVERT: A 350 TRP cc_start: 0.2514 (OUTLIER) cc_final: 0.2278 (m-90) REVERT: A 365 PRO cc_start: 0.7424 (Cg_endo) cc_final: 0.7109 (Cg_exo) REVERT: A 407 MET cc_start: 0.3102 (ttp) cc_final: 0.2573 (tmm) REVERT: A 433 GLU cc_start: 0.6853 (pt0) cc_final: 0.6626 (pp20) REVERT: B 100 MET cc_start: -0.1139 (ttt) cc_final: -0.1848 (mmt) REVERT: B 180 MET cc_start: 0.6574 (mtt) cc_final: 0.6314 (mtt) REVERT: B 209 ASP cc_start: 0.3032 (t70) cc_final: 0.2727 (t0) REVERT: B 211 ARG cc_start: 0.5805 (mtt180) cc_final: 0.5538 (ptm160) REVERT: B 216 VAL cc_start: 0.7282 (t) cc_final: 0.7073 (t) REVERT: B 359 GLN cc_start: 0.5792 (tt0) cc_final: 0.5493 (tp40) REVERT: B 433 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6296 (mt-10) REVERT: B 478 GLU cc_start: 0.7301 (tp30) cc_final: 0.6671 (pp20) REVERT: B 536 GLU cc_start: 0.5739 (tm-30) cc_final: 0.5363 (mp0) REVERT: B 550 LEU cc_start: 0.6944 (mt) cc_final: 0.6677 (tp) REVERT: B 602 GLN cc_start: 0.6729 (mt0) cc_final: 0.6500 (tp40) REVERT: C 174 TYR cc_start: 0.2832 (m-80) cc_final: 0.2628 (m-80) REVERT: C 179 GLU cc_start: 0.5254 (tm-30) cc_final: 0.5039 (tm-30) REVERT: C 211 ARG cc_start: 0.5754 (ttt180) cc_final: 0.5155 (ptm160) REVERT: C 365 PRO cc_start: 0.7073 (Cg_endo) cc_final: 0.6742 (Cg_exo) REVERT: C 407 MET cc_start: 0.1588 (tmm) cc_final: 0.1381 (tmm) REVERT: C 433 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6610 (tt0) REVERT: C 481 SER cc_start: 0.6113 (m) cc_final: 0.5688 (p) REVERT: D 300 THR cc_start: 0.5631 (OUTLIER) cc_final: 0.5391 (p) REVERT: D 365 PRO cc_start: 0.6987 (Cg_endo) cc_final: 0.6664 (Cg_exo) REVERT: D 433 GLU cc_start: 0.6637 (pt0) cc_final: 0.6382 (tt0) REVERT: E 160 ASP cc_start: 0.4629 (t70) cc_final: 0.4358 (m-30) REVERT: E 232 ARG cc_start: 0.7641 (ptt-90) cc_final: 0.7429 (ttp80) REVERT: E 238 LEU cc_start: 0.5415 (tp) cc_final: 0.5088 (mt) REVERT: E 300 THR cc_start: 0.5590 (OUTLIER) cc_final: 0.5347 (t) REVERT: E 365 PRO cc_start: 0.7578 (Cg_endo) cc_final: 0.7293 (Cg_exo) REVERT: E 423 THR cc_start: 0.5250 (m) cc_final: 0.5048 (t) REVERT: E 433 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5790 (mt-10) REVERT: E 478 GLU cc_start: 0.6959 (tp30) cc_final: 0.6528 (pp20) REVERT: E 536 GLU cc_start: 0.6133 (tm-30) cc_final: 0.5736 (mp0) REVERT: F 211 ARG cc_start: 0.4852 (mtt180) cc_final: 0.4506 (ppt170) REVERT: F 230 MET cc_start: 0.6800 (mmt) cc_final: 0.6371 (tmm) REVERT: F 300 THR cc_start: 0.6348 (OUTLIER) cc_final: 0.6118 (p) REVERT: F 312 MET cc_start: 0.7246 (tpp) cc_final: 0.6737 (mmm) REVERT: F 358 THR cc_start: 0.3294 (OUTLIER) cc_final: 0.2693 (p) REVERT: F 433 GLU cc_start: 0.6754 (pt0) cc_final: 0.6385 (tt0) REVERT: F 481 SER cc_start: 0.5861 (m) cc_final: 0.5561 (p) REVERT: G 230 MET cc_start: 0.6701 (tmm) cc_final: 0.6499 (tmm) REVERT: G 407 MET cc_start: 0.3878 (tmm) cc_final: 0.3673 (tmm) REVERT: G 433 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6625 (mt-10) REVERT: G 579 ASN cc_start: 0.6960 (t0) cc_final: 0.6601 (t0) REVERT: H 238 LEU cc_start: 0.4701 (OUTLIER) cc_final: 0.4424 (tp) REVERT: H 316 GLU cc_start: 0.7879 (tt0) cc_final: 0.7486 (tm-30) REVERT: H 376 ASP cc_start: 0.5730 (m-30) cc_final: 0.5427 (p0) REVERT: H 433 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6414 (mt-10) REVERT: H 579 ASN cc_start: 0.7045 (t0) cc_final: 0.6587 (t0) REVERT: I 183 LEU cc_start: 0.7012 (mt) cc_final: 0.6798 (mt) REVERT: I 433 GLU cc_start: 0.6702 (pt0) cc_final: 0.6395 (tt0) REVERT: I 480 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6670 (p0) REVERT: I 591 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8471 (mm) REVERT: J 238 LEU cc_start: 0.5615 (OUTLIER) cc_final: 0.5266 (tp) REVERT: J 298 GLU cc_start: 0.5605 (mt-10) cc_final: 0.5394 (mt-10) REVERT: J 300 THR cc_start: 0.6846 (OUTLIER) cc_final: 0.6469 (p) REVERT: J 407 MET cc_start: 0.2169 (tmm) cc_final: 0.1873 (tmm) REVERT: J 433 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6595 (mt-10) REVERT: J 536 GLU cc_start: 0.6239 (tm-30) cc_final: 0.5852 (mp0) REVERT: J 537 GLU cc_start: 0.5092 (mt-10) cc_final: 0.4548 (mt-10) REVERT: J 550 LEU cc_start: 0.6941 (mt) cc_final: 0.6631 (tp) REVERT: K 141 LEU cc_start: 0.1781 (OUTLIER) cc_final: 0.1543 (tp) REVERT: K 312 MET cc_start: 0.7602 (tpp) cc_final: 0.7188 (mmm) REVERT: K 316 GLU cc_start: 0.7862 (tt0) cc_final: 0.7437 (tm-30) REVERT: K 407 MET cc_start: 0.2414 (tmm) cc_final: 0.2082 (tmm) REVERT: K 423 THR cc_start: 0.5222 (p) cc_final: 0.4986 (t) REVERT: K 433 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6205 (mp0) REVERT: K 481 SER cc_start: 0.5905 (m) cc_final: 0.5561 (p) REVERT: K 579 ASN cc_start: 0.7172 (t0) cc_final: 0.6735 (t0) REVERT: L 183 LEU cc_start: 0.7331 (mt) cc_final: 0.7049 (mm) REVERT: L 251 TYR cc_start: 0.5328 (m-80) cc_final: 0.4966 (m-80) REVERT: L 365 PRO cc_start: 0.7785 (Cg_endo) cc_final: 0.7317 (Cg_exo) REVERT: L 407 MET cc_start: 0.2704 (tmm) cc_final: 0.2350 (tmm) REVERT: L 433 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: L 463 ARG cc_start: 0.2762 (OUTLIER) cc_final: 0.2396 (mtp85) REVERT: L 478 GLU cc_start: 0.7602 (tp30) cc_final: 0.7089 (pp20) REVERT: L 481 SER cc_start: 0.5682 (m) cc_final: 0.5355 (p) REVERT: L 534 THR cc_start: 0.7356 (m) cc_final: 0.6714 (m) REVERT: L 536 GLU cc_start: 0.6634 (tm-30) cc_final: 0.6199 (mp0) REVERT: L 579 ASN cc_start: 0.7030 (m-40) cc_final: 0.6658 (t0) REVERT: M 251 TYR cc_start: 0.5662 (m-80) cc_final: 0.5246 (m-80) REVERT: M 407 MET cc_start: 0.1057 (OUTLIER) cc_final: 0.0786 (tmm) REVERT: M 433 GLU cc_start: 0.6802 (pt0) cc_final: 0.6383 (mt-10) REVERT: N 209 ASP cc_start: 0.3429 (t70) cc_final: 0.3019 (t0) REVERT: N 211 ARG cc_start: 0.5965 (mtt180) cc_final: 0.5407 (ptm-80) REVERT: N 251 TYR cc_start: 0.5989 (m-80) cc_final: 0.5519 (m-80) REVERT: N 259 GLU cc_start: 0.6115 (mm-30) cc_final: 0.5656 (mt-10) REVERT: N 312 MET cc_start: 0.7783 (tpp) cc_final: 0.7582 (mmm) REVERT: N 359 GLN cc_start: 0.5870 (tt0) cc_final: 0.5543 (tp40) REVERT: N 407 MET cc_start: 0.4425 (ttp) cc_final: 0.3720 (tmm) REVERT: N 423 THR cc_start: 0.5529 (p) cc_final: 0.5033 (t) REVERT: N 433 GLU cc_start: 0.5528 (pp20) cc_final: 0.5250 (mt-10) REVERT: N 579 ASN cc_start: 0.7463 (t0) cc_final: 0.6946 (t0) REVERT: O 209 ASP cc_start: 0.3537 (t0) cc_final: 0.3261 (t0) REVERT: O 251 TYR cc_start: 0.5514 (m-80) cc_final: 0.5051 (m-80) REVERT: O 259 GLU cc_start: 0.6071 (mm-30) cc_final: 0.5574 (mt-10) REVERT: O 300 THR cc_start: 0.6196 (OUTLIER) cc_final: 0.5908 (p) REVERT: O 312 MET cc_start: 0.7807 (tpp) cc_final: 0.7396 (mmm) REVERT: O 429 MET cc_start: 0.5250 (mmm) cc_final: 0.4955 (mmm) REVERT: O 433 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5931 (mt-10) REVERT: O 478 GLU cc_start: 0.7109 (tp30) cc_final: 0.6720 (pp20) REVERT: O 534 THR cc_start: 0.7156 (m) cc_final: 0.6706 (m) REVERT: O 536 GLU cc_start: 0.6355 (tm-30) cc_final: 0.5663 (mp0) REVERT: O 579 ASN cc_start: 0.7262 (m-40) cc_final: 0.7050 (t0) outliers start: 244 outliers final: 154 residues processed: 939 average time/residue: 0.5003 time to fit residues: 820.2131 Evaluate side-chains 836 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 658 time to evaluate : 4.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 559 ASN Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 530 MET Chi-restraints excluded: chain H residue 613 VAL Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 350 TRP Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 591 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 465 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain K residue 433 GLU Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 425 SER Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 463 ARG Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 529 LEU Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 445 GLN Chi-restraints excluded: chain N residue 460 THR Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 234 optimal weight: 20.0000 chunk 626 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 408 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 696 optimal weight: 1.9990 chunk 578 optimal weight: 4.9990 chunk 322 optimal weight: 2.9990 chunk 57 optimal weight: 30.0000 chunk 230 optimal weight: 0.8980 chunk 365 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN D 188 ASN D 233 GLN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN F 233 GLN F 612 GLN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN K 188 ASN ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 602 GLN L 392 ASN ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN M 533 GLN ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 602 GLN ** N 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 602 GLN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3284 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 55485 Z= 0.291 Angle : 0.725 12.369 75255 Z= 0.368 Chirality : 0.048 0.260 9120 Planarity : 0.006 0.085 9855 Dihedral : 5.769 54.513 7792 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.83 % Favored : 93.75 % Rotamer: Outliers : 4.43 % Allowed : 21.46 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -1.84 (0.09), residues: 7200 helix: 0.38 (0.11), residues: 2025 sheet: -1.51 (0.10), residues: 2610 loop : -2.03 (0.11), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 350 HIS 0.005 0.002 HIS G 133 PHE 0.027 0.002 PHE J 592 TYR 0.023 0.002 TYR B 134 ARG 0.008 0.001 ARG L 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 703 time to evaluate : 4.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.6846 (mtm) cc_final: 0.6617 (mtm) REVERT: A 365 PRO cc_start: 0.7259 (Cg_endo) cc_final: 0.6849 (Cg_exo) REVERT: B 209 ASP cc_start: 0.3525 (t70) cc_final: 0.3062 (t0) REVERT: B 211 ARG cc_start: 0.5873 (mtt180) cc_final: 0.5540 (ptm160) REVERT: B 238 LEU cc_start: 0.4654 (pt) cc_final: 0.3857 (tp) REVERT: B 359 GLN cc_start: 0.5834 (tt0) cc_final: 0.5567 (tp40) REVERT: B 407 MET cc_start: 0.0567 (tmm) cc_final: 0.0244 (tmm) REVERT: B 433 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6118 (mt-10) REVERT: B 536 GLU cc_start: 0.5958 (tm-30) cc_final: 0.5568 (mp0) REVERT: B 550 LEU cc_start: 0.6952 (mt) cc_final: 0.6723 (tp) REVERT: B 593 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6859 (ttt-90) REVERT: C 211 ARG cc_start: 0.5838 (ttt180) cc_final: 0.5211 (ptm160) REVERT: C 238 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5462 (tp) REVERT: C 365 PRO cc_start: 0.7084 (Cg_endo) cc_final: 0.6758 (Cg_exo) REVERT: C 407 MET cc_start: 0.2047 (tmm) cc_final: 0.1826 (tmm) REVERT: C 433 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6641 (mt-10) REVERT: C 481 SER cc_start: 0.5862 (m) cc_final: 0.5531 (p) REVERT: D 174 TYR cc_start: 0.3852 (m-80) cc_final: 0.3648 (m-80) REVERT: D 259 GLU cc_start: 0.6159 (mm-30) cc_final: 0.5954 (pt0) REVERT: D 365 PRO cc_start: 0.7119 (Cg_endo) cc_final: 0.6783 (Cg_exo) REVERT: D 433 GLU cc_start: 0.6382 (pt0) cc_final: 0.5976 (mt-10) REVERT: E 160 ASP cc_start: 0.4524 (t70) cc_final: 0.4238 (m-30) REVERT: E 232 ARG cc_start: 0.7617 (ptt-90) cc_final: 0.7409 (ttp80) REVERT: E 365 PRO cc_start: 0.7621 (Cg_endo) cc_final: 0.7335 (Cg_exo) REVERT: E 433 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5597 (mt-10) REVERT: E 478 GLU cc_start: 0.6946 (tp30) cc_final: 0.6551 (tm-30) REVERT: E 536 GLU cc_start: 0.6036 (tm-30) cc_final: 0.5612 (mp0) REVERT: F 102 THR cc_start: 0.2704 (OUTLIER) cc_final: 0.2482 (t) REVERT: F 160 ASP cc_start: 0.6442 (t70) cc_final: 0.5997 (m-30) REVERT: F 230 MET cc_start: 0.6793 (mmt) cc_final: 0.6348 (tmm) REVERT: F 300 THR cc_start: 0.6194 (OUTLIER) cc_final: 0.5937 (t) REVERT: F 312 MET cc_start: 0.7169 (tpp) cc_final: 0.6708 (mmm) REVERT: F 433 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6426 (mt-10) REVERT: F 481 SER cc_start: 0.5853 (m) cc_final: 0.5528 (p) REVERT: F 579 ASN cc_start: 0.7040 (t0) cc_final: 0.6714 (t0) REVERT: G 297 ASP cc_start: 0.4630 (OUTLIER) cc_final: 0.4376 (m-30) REVERT: G 407 MET cc_start: 0.4018 (tmm) cc_final: 0.3797 (tmm) REVERT: G 433 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: G 579 ASN cc_start: 0.7369 (t0) cc_final: 0.7050 (t0) REVERT: H 100 MET cc_start: 0.1177 (ttt) cc_final: 0.0562 (mmm) REVERT: H 238 LEU cc_start: 0.4949 (OUTLIER) cc_final: 0.4668 (tp) REVERT: H 316 GLU cc_start: 0.7957 (tt0) cc_final: 0.7564 (tm-30) REVERT: H 376 ASP cc_start: 0.5719 (m-30) cc_final: 0.5462 (p0) REVERT: H 407 MET cc_start: 0.3541 (tmm) cc_final: 0.3241 (tmm) REVERT: H 433 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6063 (mt-10) REVERT: H 579 ASN cc_start: 0.6962 (t0) cc_final: 0.6508 (t0) REVERT: I 407 MET cc_start: 0.1548 (tpt) cc_final: 0.1325 (tpp) REVERT: I 433 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6395 (tt0) REVERT: J 238 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5512 (tp) REVERT: J 300 THR cc_start: 0.6715 (OUTLIER) cc_final: 0.6469 (p) REVERT: J 407 MET cc_start: 0.2878 (tmm) cc_final: 0.2612 (tmm) REVERT: J 433 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: J 536 GLU cc_start: 0.6244 (tm-30) cc_final: 0.5871 (mp0) REVERT: J 537 GLU cc_start: 0.5239 (mt-10) cc_final: 0.4676 (mt-10) REVERT: K 312 MET cc_start: 0.7456 (tpp) cc_final: 0.7017 (mmm) REVERT: K 316 GLU cc_start: 0.7863 (tt0) cc_final: 0.7456 (tm-30) REVERT: K 407 MET cc_start: 0.2441 (tmm) cc_final: 0.2122 (tmm) REVERT: K 481 SER cc_start: 0.5977 (m) cc_final: 0.5615 (p) REVERT: K 579 ASN cc_start: 0.7295 (t0) cc_final: 0.6873 (t0) REVERT: L 251 TYR cc_start: 0.5548 (m-80) cc_final: 0.5248 (m-80) REVERT: L 365 PRO cc_start: 0.7559 (Cg_endo) cc_final: 0.7090 (Cg_exo) REVERT: L 407 MET cc_start: 0.2898 (tmm) cc_final: 0.2544 (tmm) REVERT: L 433 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6595 (mt-10) REVERT: L 463 ARG cc_start: 0.2972 (OUTLIER) cc_final: 0.2670 (mtp85) REVERT: L 478 GLU cc_start: 0.7406 (tp30) cc_final: 0.6894 (pp20) REVERT: L 481 SER cc_start: 0.5604 (m) cc_final: 0.5259 (p) REVERT: L 579 ASN cc_start: 0.7228 (m-40) cc_final: 0.6830 (t0) REVERT: M 251 TYR cc_start: 0.5859 (m-80) cc_final: 0.5433 (m-80) REVERT: M 365 PRO cc_start: 0.7218 (Cg_endo) cc_final: 0.6677 (Cg_exo) REVERT: M 407 MET cc_start: 0.1420 (tmm) cc_final: 0.1083 (tmm) REVERT: M 433 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6143 (mt-10) REVERT: N 174 TYR cc_start: 0.2586 (m-80) cc_final: 0.2337 (m-80) REVERT: N 211 ARG cc_start: 0.6451 (mtt180) cc_final: 0.5793 (ptm160) REVERT: N 251 TYR cc_start: 0.5765 (m-80) cc_final: 0.5371 (m-80) REVERT: N 312 MET cc_start: 0.7754 (tpp) cc_final: 0.7436 (mmm) REVERT: N 433 GLU cc_start: 0.5561 (pp20) cc_final: 0.5285 (mt-10) REVERT: N 579 ASN cc_start: 0.7457 (t0) cc_final: 0.6936 (t0) REVERT: O 251 TYR cc_start: 0.5184 (m-80) cc_final: 0.4777 (m-80) REVERT: O 259 GLU cc_start: 0.6239 (mm-30) cc_final: 0.5724 (mt-10) REVERT: O 312 MET cc_start: 0.7771 (tpp) cc_final: 0.7459 (mmm) REVERT: O 429 MET cc_start: 0.5550 (mmm) cc_final: 0.5305 (mmm) REVERT: O 433 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6016 (mt-10) REVERT: O 536 GLU cc_start: 0.6466 (tm-30) cc_final: 0.6186 (tm-30) REVERT: O 579 ASN cc_start: 0.7251 (m-40) cc_final: 0.7037 (t0) outliers start: 268 outliers final: 179 residues processed: 907 average time/residue: 0.5558 time to fit residues: 879.1478 Evaluate side-chains 822 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 623 time to evaluate : 4.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 298 GLU Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 559 ASN Chi-restraints excluded: chain H residue 613 VAL Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 298 GLU Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 350 TRP Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 531 ASP Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 524 VAL Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 559 ASN Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 559 ASN Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 425 SER Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 463 ARG Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 529 LEU Chi-restraints excluded: chain L residue 550 LEU Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 182 ARG Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 530 MET Chi-restraints excluded: chain M residue 557 THR Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 445 GLN Chi-restraints excluded: chain N residue 460 THR Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 512 VAL Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 573 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 337 GLU Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 512 VAL Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 557 THR Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 671 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 396 optimal weight: 30.0000 chunk 508 optimal weight: 5.9990 chunk 394 optimal weight: 0.0770 chunk 586 optimal weight: 5.9990 chunk 389 optimal weight: 20.0000 chunk 693 optimal weight: 1.9990 chunk 434 optimal weight: 10.0000 chunk 423 optimal weight: 0.9990 chunk 320 optimal weight: 0.7980 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN I 301 ASN J 533 GLN ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN M 533 GLN ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3286 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 55485 Z= 0.186 Angle : 0.674 11.211 75255 Z= 0.336 Chirality : 0.046 0.293 9120 Planarity : 0.005 0.080 9855 Dihedral : 5.500 53.610 7790 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.93 % Favored : 95.65 % Rotamer: Outliers : 3.92 % Allowed : 22.91 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -1.67 (0.10), residues: 7200 helix: 0.55 (0.11), residues: 2010 sheet: -1.60 (0.09), residues: 2760 loop : -1.68 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 405 HIS 0.005 0.002 HIS A 133 PHE 0.020 0.001 PHE J 592 TYR 0.029 0.002 TYR G 581 ARG 0.009 0.000 ARG O 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 693 time to evaluate : 4.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7079 (mtm) cc_final: 0.6848 (mtm) REVERT: A 365 PRO cc_start: 0.7105 (Cg_endo) cc_final: 0.6679 (Cg_exo) REVERT: A 481 SER cc_start: 0.5760 (m) cc_final: 0.5373 (p) REVERT: B 209 ASP cc_start: 0.3429 (t70) cc_final: 0.2968 (t0) REVERT: B 211 ARG cc_start: 0.5935 (mtt180) cc_final: 0.5572 (ptm160) REVERT: B 238 LEU cc_start: 0.4738 (pt) cc_final: 0.4002 (tp) REVERT: B 407 MET cc_start: 0.0987 (tmm) cc_final: 0.0627 (tmm) REVERT: B 433 GLU cc_start: 0.6781 (pt0) cc_final: 0.6352 (mt-10) REVERT: B 536 GLU cc_start: 0.5767 (tm-30) cc_final: 0.5494 (mp0) REVERT: B 550 LEU cc_start: 0.7020 (mt) cc_final: 0.6770 (tp) REVERT: C 209 ASP cc_start: 0.2885 (t0) cc_final: 0.2551 (t0) REVERT: C 211 ARG cc_start: 0.5909 (ttt180) cc_final: 0.5250 (ptm160) REVERT: C 365 PRO cc_start: 0.7070 (Cg_endo) cc_final: 0.6723 (Cg_exo) REVERT: C 407 MET cc_start: 0.2086 (tmm) cc_final: 0.1856 (tmm) REVERT: C 433 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6727 (mt-10) REVERT: C 481 SER cc_start: 0.5777 (m) cc_final: 0.5412 (p) REVERT: C 579 ASN cc_start: 0.7690 (t0) cc_final: 0.7264 (t0) REVERT: D 174 TYR cc_start: 0.3775 (m-80) cc_final: 0.3499 (m-80) REVERT: D 180 MET cc_start: 0.6848 (mtt) cc_final: 0.6626 (mtm) REVERT: D 259 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5977 (pt0) REVERT: D 365 PRO cc_start: 0.7040 (Cg_endo) cc_final: 0.6668 (Cg_exo) REVERT: D 376 ASP cc_start: 0.5927 (OUTLIER) cc_final: 0.5648 (p0) REVERT: D 433 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5969 (mt-10) REVERT: E 160 ASP cc_start: 0.4529 (t70) cc_final: 0.4274 (m-30) REVERT: E 232 ARG cc_start: 0.7607 (ptt-90) cc_final: 0.7395 (ttp80) REVERT: E 300 THR cc_start: 0.6031 (OUTLIER) cc_final: 0.5809 (t) REVERT: E 365 PRO cc_start: 0.7561 (Cg_endo) cc_final: 0.7259 (Cg_exo) REVERT: E 433 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.5485 (mt-10) REVERT: E 478 GLU cc_start: 0.7001 (tp30) cc_final: 0.6586 (pp20) REVERT: E 536 GLU cc_start: 0.6129 (tm-30) cc_final: 0.5765 (mp0) REVERT: F 160 ASP cc_start: 0.6470 (t70) cc_final: 0.6030 (m-30) REVERT: F 230 MET cc_start: 0.6751 (mmt) cc_final: 0.6322 (tmm) REVERT: F 300 THR cc_start: 0.6476 (OUTLIER) cc_final: 0.6204 (t) REVERT: F 312 MET cc_start: 0.7363 (tpp) cc_final: 0.6846 (mmm) REVERT: F 433 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6319 (mt-10) REVERT: F 579 ASN cc_start: 0.6979 (t0) cc_final: 0.6646 (t0) REVERT: G 100 MET cc_start: 0.2487 (mmm) cc_final: 0.1665 (mmm) REVERT: G 160 ASP cc_start: 0.6240 (t70) cc_final: 0.5838 (t70) REVERT: G 407 MET cc_start: 0.4118 (tmm) cc_final: 0.3907 (tmm) REVERT: G 433 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6828 (mt-10) REVERT: G 579 ASN cc_start: 0.7478 (t0) cc_final: 0.7173 (t0) REVERT: H 100 MET cc_start: 0.1147 (ttt) cc_final: 0.0518 (mmm) REVERT: H 316 GLU cc_start: 0.7823 (tt0) cc_final: 0.7433 (tm-30) REVERT: H 376 ASP cc_start: 0.5656 (m-30) cc_final: 0.5449 (p0) REVERT: H 433 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6049 (mt-10) REVERT: H 579 ASN cc_start: 0.6950 (t0) cc_final: 0.6505 (t0) REVERT: H 591 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8378 (tp) REVERT: I 241 GLN cc_start: 0.4060 (OUTLIER) cc_final: 0.3811 (pm20) REVERT: I 433 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6379 (tt0) REVERT: J 238 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5569 (tt) REVERT: J 300 THR cc_start: 0.6817 (OUTLIER) cc_final: 0.6452 (p) REVERT: J 407 MET cc_start: 0.2955 (tmm) cc_final: 0.2509 (tmm) REVERT: J 433 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6751 (mt-10) REVERT: J 481 SER cc_start: 0.5538 (m) cc_final: 0.5205 (p) REVERT: J 536 GLU cc_start: 0.6348 (tm-30) cc_final: 0.6028 (mp0) REVERT: J 537 GLU cc_start: 0.5153 (mt-10) cc_final: 0.4596 (mt-10) REVERT: J 579 ASN cc_start: 0.7158 (t0) cc_final: 0.6836 (t0) REVERT: K 238 LEU cc_start: 0.4856 (pp) cc_final: 0.4526 (tt) REVERT: K 312 MET cc_start: 0.7411 (tpp) cc_final: 0.6895 (mmm) REVERT: K 316 GLU cc_start: 0.7825 (tt0) cc_final: 0.7406 (tm-30) REVERT: K 407 MET cc_start: 0.2950 (tmm) cc_final: 0.2672 (tmm) REVERT: K 579 ASN cc_start: 0.7291 (t0) cc_final: 0.6882 (t0) REVERT: L 172 LEU cc_start: 0.5087 (OUTLIER) cc_final: 0.4721 (mt) REVERT: L 251 TYR cc_start: 0.5255 (m-80) cc_final: 0.5014 (m-80) REVERT: L 365 PRO cc_start: 0.7479 (Cg_endo) cc_final: 0.7011 (Cg_exo) REVERT: L 407 MET cc_start: 0.3223 (tmm) cc_final: 0.2899 (tmm) REVERT: L 463 ARG cc_start: 0.2940 (OUTLIER) cc_final: 0.2584 (mtp85) REVERT: L 478 GLU cc_start: 0.7403 (tp30) cc_final: 0.6881 (pp20) REVERT: L 579 ASN cc_start: 0.7228 (m-40) cc_final: 0.6862 (t0) REVERT: M 251 TYR cc_start: 0.5355 (m-80) cc_final: 0.5074 (m-80) REVERT: M 365 PRO cc_start: 0.6851 (Cg_endo) cc_final: 0.6340 (Cg_exo) REVERT: M 407 MET cc_start: 0.1480 (tmm) cc_final: 0.1119 (tmm) REVERT: M 433 GLU cc_start: 0.6623 (pt0) cc_final: 0.6184 (mt-10) REVERT: N 211 ARG cc_start: 0.5463 (mtt180) cc_final: 0.4988 (ptm-80) REVERT: N 238 LEU cc_start: 0.5053 (OUTLIER) cc_final: 0.4672 (tt) REVERT: N 251 TYR cc_start: 0.5679 (m-80) cc_final: 0.5194 (m-80) REVERT: N 312 MET cc_start: 0.7700 (tpp) cc_final: 0.7405 (mmm) REVERT: N 579 ASN cc_start: 0.7503 (t0) cc_final: 0.6997 (t0) REVERT: O 251 TYR cc_start: 0.4941 (m-80) cc_final: 0.4434 (m-80) REVERT: O 312 MET cc_start: 0.7759 (tpp) cc_final: 0.7450 (mmm) REVERT: O 376 ASP cc_start: 0.5810 (m-30) cc_final: 0.5517 (p0) REVERT: O 407 MET cc_start: 0.1726 (ttp) cc_final: 0.1408 (tmm) REVERT: O 429 MET cc_start: 0.5382 (mmm) cc_final: 0.5159 (mmm) REVERT: O 433 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5987 (mt-10) REVERT: O 481 SER cc_start: 0.6002 (m) cc_final: 0.5493 (p) REVERT: O 536 GLU cc_start: 0.6242 (tm-30) cc_final: 0.6006 (tm-30) REVERT: O 579 ASN cc_start: 0.7295 (m-40) cc_final: 0.7087 (t0) outliers start: 237 outliers final: 161 residues processed: 871 average time/residue: 0.4875 time to fit residues: 748.0916 Evaluate side-chains 816 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 636 time to evaluate : 4.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 298 GLU Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 349 GLN Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 559 ASN Chi-restraints excluded: chain H residue 591 LEU Chi-restraints excluded: chain H residue 613 VAL Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 350 TRP Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 531 ASP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 533 GLN Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 463 ARG Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 529 LEU Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 445 GLN Chi-restraints excluded: chain N residue 460 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 573 THR Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 257 MET Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 512 VAL Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 429 optimal weight: 10.0000 chunk 277 optimal weight: 0.6980 chunk 414 optimal weight: 5.9990 chunk 209 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 441 optimal weight: 7.9990 chunk 472 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 545 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 GLN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN E 533 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN H 533 GLN H 602 GLN I 133 HIS J 308 GLN K 213 ASN ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN M 213 ASN M 533 GLN ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3290 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 55485 Z= 0.365 Angle : 0.808 15.332 75255 Z= 0.406 Chirality : 0.050 0.288 9120 Planarity : 0.006 0.086 9855 Dihedral : 5.995 54.809 7790 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.50 % Favored : 92.22 % Rotamer: Outliers : 3.94 % Allowed : 23.23 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -1.98 (0.09), residues: 7200 helix: 0.36 (0.11), residues: 2040 sheet: -1.50 (0.10), residues: 2505 loop : -2.34 (0.11), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 350 HIS 0.006 0.002 HIS G 133 PHE 0.026 0.003 PHE H 507 TYR 0.028 0.003 TYR N 174 ARG 0.013 0.001 ARG O 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 665 time to evaluate : 4.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.2456 (tt) cc_final: 0.2204 (tt) REVERT: A 365 PRO cc_start: 0.7143 (Cg_endo) cc_final: 0.6748 (Cg_exo) REVERT: A 433 GLU cc_start: 0.6555 (mt-10) cc_final: 0.6153 (tm-30) REVERT: B 209 ASP cc_start: 0.3063 (t70) cc_final: 0.2520 (t0) REVERT: B 211 ARG cc_start: 0.5858 (mtt180) cc_final: 0.5445 (ptm160) REVERT: B 433 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6397 (mt-10) REVERT: B 536 GLU cc_start: 0.5913 (tm-30) cc_final: 0.5498 (mp0) REVERT: C 209 ASP cc_start: 0.2844 (t0) cc_final: 0.2150 (t0) REVERT: C 211 ARG cc_start: 0.5875 (ttt180) cc_final: 0.5310 (ptm160) REVERT: C 238 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5517 (tp) REVERT: C 365 PRO cc_start: 0.7227 (Cg_endo) cc_final: 0.6915 (Cg_exo) REVERT: C 407 MET cc_start: 0.2456 (tmm) cc_final: 0.2188 (tmm) REVERT: C 433 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6805 (mt-10) REVERT: C 481 SER cc_start: 0.5889 (m) cc_final: 0.5497 (p) REVERT: C 579 ASN cc_start: 0.7476 (t0) cc_final: 0.7136 (t0) REVERT: D 180 MET cc_start: 0.6867 (mtt) cc_final: 0.6321 (mtm) REVERT: D 259 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6189 (pt0) REVERT: D 365 PRO cc_start: 0.7197 (Cg_endo) cc_final: 0.6841 (Cg_exo) REVERT: D 376 ASP cc_start: 0.5855 (OUTLIER) cc_final: 0.5634 (p0) REVERT: D 433 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5919 (mt-10) REVERT: E 160 ASP cc_start: 0.4553 (t70) cc_final: 0.4266 (m-30) REVERT: E 365 PRO cc_start: 0.7699 (Cg_endo) cc_final: 0.7385 (Cg_exo) REVERT: E 433 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.5414 (mt-10) REVERT: E 478 GLU cc_start: 0.6811 (tp30) cc_final: 0.6401 (tm-30) REVERT: F 160 ASP cc_start: 0.6502 (t70) cc_final: 0.6079 (m-30) REVERT: F 230 MET cc_start: 0.6342 (mmt) cc_final: 0.5987 (tmm) REVERT: F 312 MET cc_start: 0.6988 (tpp) cc_final: 0.6389 (mmm) REVERT: F 433 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6287 (mt-10) REVERT: F 481 SER cc_start: 0.5900 (m) cc_final: 0.5589 (p) REVERT: F 579 ASN cc_start: 0.7046 (t0) cc_final: 0.6752 (t0) REVERT: F 593 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7578 (ttm-80) REVERT: G 160 ASP cc_start: 0.6417 (t70) cc_final: 0.5917 (t70) REVERT: G 211 ARG cc_start: 0.5829 (mtt180) cc_final: 0.4775 (ptm-80) REVERT: G 407 MET cc_start: 0.4321 (tmm) cc_final: 0.4050 (tmm) REVERT: G 433 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: G 579 ASN cc_start: 0.7527 (t0) cc_final: 0.7224 (t0) REVERT: H 174 TYR cc_start: 0.2821 (m-80) cc_final: 0.2617 (m-80) REVERT: H 238 LEU cc_start: 0.5325 (OUTLIER) cc_final: 0.4862 (tp) REVERT: H 316 GLU cc_start: 0.7995 (tt0) cc_final: 0.7586 (tm-30) REVERT: H 376 ASP cc_start: 0.5813 (m-30) cc_final: 0.5612 (p0) REVERT: H 433 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5936 (mt-10) REVERT: H 579 ASN cc_start: 0.6997 (t0) cc_final: 0.6536 (t0) REVERT: H 591 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8429 (tp) REVERT: I 158 ARG cc_start: 0.3038 (OUTLIER) cc_final: 0.1837 (mmt180) REVERT: I 413 SER cc_start: 0.5452 (m) cc_final: 0.5129 (t) REVERT: I 433 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6472 (mt-10) REVERT: J 238 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5611 (tp) REVERT: J 300 THR cc_start: 0.6626 (OUTLIER) cc_final: 0.6384 (p) REVERT: J 407 MET cc_start: 0.3289 (tmm) cc_final: 0.2853 (tmm) REVERT: J 433 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6491 (mt-10) REVERT: K 211 ARG cc_start: 0.6806 (mtt180) cc_final: 0.6051 (ptm-80) REVERT: K 301 ASN cc_start: 0.2773 (t0) cc_final: 0.2391 (t0) REVERT: K 312 MET cc_start: 0.7287 (tpp) cc_final: 0.6854 (mmm) REVERT: K 316 GLU cc_start: 0.7914 (tt0) cc_final: 0.7508 (tm-30) REVERT: K 407 MET cc_start: 0.2943 (tmm) cc_final: 0.2663 (tmm) REVERT: K 433 GLU cc_start: 0.6028 (tm-30) cc_final: 0.5661 (mt-10) REVERT: K 481 SER cc_start: 0.5804 (m) cc_final: 0.5410 (p) REVERT: L 251 TYR cc_start: 0.5010 (m-80) cc_final: 0.4707 (m-80) REVERT: L 365 PRO cc_start: 0.7510 (Cg_endo) cc_final: 0.7062 (Cg_exo) REVERT: L 407 MET cc_start: 0.3208 (tmm) cc_final: 0.2767 (tmm) REVERT: L 481 SER cc_start: 0.5890 (m) cc_final: 0.5583 (p) REVERT: L 579 ASN cc_start: 0.7323 (m-40) cc_final: 0.6954 (t0) REVERT: M 251 TYR cc_start: 0.5189 (m-80) cc_final: 0.4983 (m-80) REVERT: M 407 MET cc_start: 0.1597 (OUTLIER) cc_final: 0.1179 (tmm) REVERT: M 433 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5828 (mt-10) REVERT: N 211 ARG cc_start: 0.6136 (mtt180) cc_final: 0.5370 (ptm-80) REVERT: N 251 TYR cc_start: 0.5548 (m-80) cc_final: 0.5250 (m-80) REVERT: N 312 MET cc_start: 0.7645 (tpp) cc_final: 0.7225 (mmm) REVERT: N 376 ASP cc_start: 0.5674 (m-30) cc_final: 0.5460 (p0) REVERT: N 429 MET cc_start: 0.5806 (mmm) cc_final: 0.5553 (mmm) REVERT: N 579 ASN cc_start: 0.7549 (t0) cc_final: 0.7093 (t0) REVERT: O 251 TYR cc_start: 0.5008 (m-80) cc_final: 0.4716 (m-80) REVERT: O 312 MET cc_start: 0.7583 (tpp) cc_final: 0.7316 (mmm) REVERT: O 407 MET cc_start: 0.1666 (ttp) cc_final: 0.1380 (tmm) REVERT: O 429 MET cc_start: 0.5677 (mmm) cc_final: 0.5433 (mmm) REVERT: O 433 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.6099 (mt-10) REVERT: O 579 ASN cc_start: 0.7280 (m-40) cc_final: 0.7068 (t0) outliers start: 238 outliers final: 169 residues processed: 845 average time/residue: 0.4833 time to fit residues: 711.7461 Evaluate side-chains 783 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 594 time to evaluate : 4.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 593 ARG Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 349 GLN Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 559 ASN Chi-restraints excluded: chain H residue 591 LEU Chi-restraints excluded: chain H residue 613 VAL Chi-restraints excluded: chain I residue 158 ARG Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 298 GLU Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 531 ASP Chi-restraints excluded: chain I residue 557 THR Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 503 LEU Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 567 MET Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 425 SER Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 550 LEU Chi-restraints excluded: chain L residue 557 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 292 LEU Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 445 GLN Chi-restraints excluded: chain N residue 460 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 573 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 337 GLU Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 482 VAL Chi-restraints excluded: chain O residue 512 VAL Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 631 optimal weight: 3.9990 chunk 664 optimal weight: 30.0000 chunk 606 optimal weight: 0.9980 chunk 646 optimal weight: 10.0000 chunk 389 optimal weight: 8.9990 chunk 281 optimal weight: 8.9990 chunk 507 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 584 optimal weight: 0.7980 chunk 611 optimal weight: 0.5980 chunk 644 optimal weight: 0.8980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 308 GLN ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN M 488 GLN M 533 GLN ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3291 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 55485 Z= 0.217 Angle : 0.712 12.624 75255 Z= 0.353 Chirality : 0.047 0.313 9120 Planarity : 0.005 0.107 9855 Dihedral : 5.648 45.505 7786 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.94 % Favored : 94.79 % Rotamer: Outliers : 3.44 % Allowed : 24.14 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -1.74 (0.10), residues: 7200 helix: 0.51 (0.11), residues: 2055 sheet: -1.33 (0.10), residues: 2505 loop : -2.20 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 405 HIS 0.006 0.001 HIS G 133 PHE 0.014 0.002 PHE B 554 TYR 0.031 0.002 TYR L 174 ARG 0.007 0.001 ARG E 611 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 651 time to evaluate : 4.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 PRO cc_start: 0.7095 (Cg_endo) cc_final: 0.6669 (Cg_exo) REVERT: A 433 GLU cc_start: 0.6509 (mt-10) cc_final: 0.6130 (tm-30) REVERT: A 481 SER cc_start: 0.5673 (m) cc_final: 0.5204 (p) REVERT: B 174 TYR cc_start: 0.3239 (m-80) cc_final: 0.1912 (t80) REVERT: B 209 ASP cc_start: 0.3081 (t70) cc_final: 0.2654 (t0) REVERT: B 211 ARG cc_start: 0.5963 (mtt180) cc_final: 0.5564 (ptm160) REVERT: B 433 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6424 (mt-10) REVERT: B 536 GLU cc_start: 0.5916 (tm-30) cc_final: 0.5648 (mp0) REVERT: C 174 TYR cc_start: 0.3025 (m-80) cc_final: 0.2822 (m-80) REVERT: C 209 ASP cc_start: 0.3184 (t70) cc_final: 0.2869 (t0) REVERT: C 211 ARG cc_start: 0.6131 (ttt180) cc_final: 0.5672 (ptm160) REVERT: C 238 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5296 (tp) REVERT: C 365 PRO cc_start: 0.7228 (Cg_endo) cc_final: 0.6892 (Cg_exo) REVERT: C 407 MET cc_start: 0.2788 (tmm) cc_final: 0.2537 (tmm) REVERT: C 433 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6613 (mt-10) REVERT: C 579 ASN cc_start: 0.7587 (t0) cc_final: 0.7208 (t0) REVERT: D 174 TYR cc_start: 0.3680 (m-80) cc_final: 0.3410 (m-80) REVERT: D 180 MET cc_start: 0.6945 (mtt) cc_final: 0.6429 (mtm) REVERT: D 365 PRO cc_start: 0.7173 (Cg_endo) cc_final: 0.6787 (Cg_exo) REVERT: D 433 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5919 (mt-10) REVERT: D 530 MET cc_start: 0.4262 (mpp) cc_final: 0.3793 (ttm) REVERT: D 567 MET cc_start: 0.3615 (mmt) cc_final: 0.3285 (mmt) REVERT: D 579 ASN cc_start: 0.7551 (t0) cc_final: 0.7234 (t0) REVERT: E 160 ASP cc_start: 0.4567 (t70) cc_final: 0.4286 (m-30) REVERT: E 232 ARG cc_start: 0.7607 (ptt-90) cc_final: 0.7394 (ttp80) REVERT: E 365 PRO cc_start: 0.7632 (Cg_endo) cc_final: 0.7317 (Cg_exo) REVERT: E 433 GLU cc_start: 0.5778 (OUTLIER) cc_final: 0.5347 (mt-10) REVERT: E 478 GLU cc_start: 0.6925 (tp30) cc_final: 0.6523 (pp20) REVERT: E 536 GLU cc_start: 0.6482 (tm-30) cc_final: 0.5962 (mp0) REVERT: F 160 ASP cc_start: 0.6382 (t70) cc_final: 0.5970 (t0) REVERT: F 230 MET cc_start: 0.6418 (mmt) cc_final: 0.6079 (tmm) REVERT: F 312 MET cc_start: 0.6978 (tpp) cc_final: 0.6387 (mmm) REVERT: F 433 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.6072 (mt-10) REVERT: G 134 TYR cc_start: 0.3674 (m-80) cc_final: 0.3464 (m-80) REVERT: G 160 ASP cc_start: 0.6457 (t70) cc_final: 0.5956 (t70) REVERT: G 407 MET cc_start: 0.4304 (tmm) cc_final: 0.4036 (tmm) REVERT: G 433 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6702 (mt-10) REVERT: G 579 ASN cc_start: 0.7488 (t0) cc_final: 0.7182 (t0) REVERT: H 100 MET cc_start: 0.1248 (ttt) cc_final: -0.0435 (mtp) REVERT: H 238 LEU cc_start: 0.5298 (OUTLIER) cc_final: 0.5008 (tp) REVERT: H 316 GLU cc_start: 0.7913 (tt0) cc_final: 0.7486 (tm-30) REVERT: H 433 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6009 (mt-10) REVERT: H 579 ASN cc_start: 0.6928 (t0) cc_final: 0.6458 (t0) REVERT: H 591 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8459 (tp) REVERT: H 610 ASP cc_start: 0.6000 (t0) cc_final: 0.5641 (t0) REVERT: I 158 ARG cc_start: 0.2877 (OUTLIER) cc_final: 0.1622 (mmt180) REVERT: I 433 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6330 (mt-10) REVERT: J 238 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5680 (tp) REVERT: J 407 MET cc_start: 0.3441 (tmm) cc_final: 0.3086 (tmm) REVERT: J 433 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6675 (mt-10) REVERT: J 481 SER cc_start: 0.5191 (m) cc_final: 0.4814 (p) REVERT: J 536 GLU cc_start: 0.6456 (tm-30) cc_final: 0.6012 (mp0) REVERT: K 238 LEU cc_start: 0.4908 (pp) cc_final: 0.4543 (tp) REVERT: K 312 MET cc_start: 0.7295 (tpp) cc_final: 0.6847 (mmm) REVERT: K 316 GLU cc_start: 0.7902 (tt0) cc_final: 0.7486 (tm-30) REVERT: K 407 MET cc_start: 0.2993 (tmm) cc_final: 0.2715 (tmm) REVERT: K 433 GLU cc_start: 0.6351 (tm-30) cc_final: 0.6026 (mt-10) REVERT: K 579 ASN cc_start: 0.7086 (t0) cc_final: 0.6747 (t0) REVERT: L 172 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4559 (mt) REVERT: L 251 TYR cc_start: 0.5110 (m-80) cc_final: 0.4848 (m-80) REVERT: L 407 MET cc_start: 0.2972 (tmm) cc_final: 0.2594 (tmm) REVERT: L 433 GLU cc_start: 0.6423 (mt-10) cc_final: 0.6137 (mm-30) REVERT: L 579 ASN cc_start: 0.7285 (m-40) cc_final: 0.6938 (t0) REVERT: M 251 TYR cc_start: 0.5209 (m-80) cc_final: 0.4996 (m-80) REVERT: M 407 MET cc_start: 0.1648 (OUTLIER) cc_final: 0.1215 (tmm) REVERT: M 433 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6216 (mt-10) REVERT: N 211 ARG cc_start: 0.6233 (mtt180) cc_final: 0.5607 (ptm-80) REVERT: N 251 TYR cc_start: 0.5548 (m-80) cc_final: 0.5159 (m-80) REVERT: N 312 MET cc_start: 0.7664 (tpp) cc_final: 0.7290 (mmm) REVERT: N 429 MET cc_start: 0.5723 (mmm) cc_final: 0.5472 (mmm) REVERT: N 579 ASN cc_start: 0.7568 (t0) cc_final: 0.7151 (t0) REVERT: O 251 TYR cc_start: 0.4963 (m-80) cc_final: 0.4492 (m-80) REVERT: O 312 MET cc_start: 0.7570 (tpp) cc_final: 0.7314 (mmm) REVERT: O 376 ASP cc_start: 0.5766 (m-30) cc_final: 0.5469 (p0) REVERT: O 407 MET cc_start: 0.1888 (ttp) cc_final: 0.1613 (tmm) REVERT: O 429 MET cc_start: 0.5901 (mmm) cc_final: 0.5632 (mmm) REVERT: O 433 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6108 (mt-10) REVERT: O 481 SER cc_start: 0.5910 (m) cc_final: 0.5415 (p) REVERT: O 579 ASN cc_start: 0.7264 (m-40) cc_final: 0.7062 (t0) outliers start: 208 outliers final: 152 residues processed: 809 average time/residue: 0.4978 time to fit residues: 701.6739 Evaluate side-chains 773 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 603 time to evaluate : 4.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 349 GLN Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 559 ASN Chi-restraints excluded: chain H residue 573 THR Chi-restraints excluded: chain H residue 591 LEU Chi-restraints excluded: chain H residue 613 VAL Chi-restraints excluded: chain I residue 158 ARG Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 298 GLU Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 531 ASP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 308 GLN Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 533 GLN Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain N residue 306 THR Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 445 GLN Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 573 THR Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 257 MET Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 482 VAL Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 424 optimal weight: 4.9990 chunk 683 optimal weight: 8.9990 chunk 417 optimal weight: 0.9980 chunk 324 optimal weight: 0.9980 chunk 475 optimal weight: 1.9990 chunk 717 optimal weight: 4.9990 chunk 660 optimal weight: 5.9990 chunk 571 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 441 optimal weight: 7.9990 chunk 350 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 308 GLN ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN L 595 GLN M 488 GLN M 533 GLN ** N 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3294 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 55485 Z= 0.210 Angle : 0.706 12.201 75255 Z= 0.349 Chirality : 0.047 0.383 9120 Planarity : 0.005 0.097 9855 Dihedral : 5.504 44.924 7786 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.14 % Favored : 93.60 % Rotamer: Outliers : 3.06 % Allowed : 24.75 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -1.64 (0.10), residues: 7200 helix: 0.58 (0.11), residues: 2055 sheet: -1.26 (0.11), residues: 2505 loop : -2.15 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 405 HIS 0.006 0.001 HIS G 133 PHE 0.031 0.002 PHE G 393 TYR 0.027 0.002 TYR L 174 ARG 0.010 0.000 ARG D 182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 629 time to evaluate : 4.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 PRO cc_start: 0.7087 (Cg_endo) cc_final: 0.6670 (Cg_exo) REVERT: A 433 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6125 (tm-30) REVERT: B 174 TYR cc_start: 0.3450 (m-80) cc_final: 0.2370 (t80) REVERT: B 209 ASP cc_start: 0.2996 (t70) cc_final: 0.2514 (t0) REVERT: B 211 ARG cc_start: 0.5841 (mtt180) cc_final: 0.5475 (ptm160) REVERT: B 433 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6409 (mt-10) REVERT: B 536 GLU cc_start: 0.5907 (tm-30) cc_final: 0.5569 (mp0) REVERT: B 593 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6790 (ttt-90) REVERT: C 209 ASP cc_start: 0.3565 (t70) cc_final: 0.3082 (t0) REVERT: C 211 ARG cc_start: 0.6157 (ttt180) cc_final: 0.5805 (ptm160) REVERT: C 238 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5268 (tp) REVERT: C 365 PRO cc_start: 0.7258 (Cg_endo) cc_final: 0.6916 (Cg_exo) REVERT: C 407 MET cc_start: 0.2818 (tmm) cc_final: 0.2565 (tmm) REVERT: C 433 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6578 (mt-10) REVERT: C 579 ASN cc_start: 0.7584 (t0) cc_final: 0.7208 (t0) REVERT: D 365 PRO cc_start: 0.7147 (Cg_endo) cc_final: 0.6751 (Cg_exo) REVERT: D 433 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5876 (mt-10) REVERT: D 530 MET cc_start: 0.4262 (mpp) cc_final: 0.3799 (ttm) REVERT: D 579 ASN cc_start: 0.7584 (t0) cc_final: 0.7285 (t0) REVERT: E 160 ASP cc_start: 0.4536 (t70) cc_final: 0.4277 (m-30) REVERT: E 232 ARG cc_start: 0.7530 (ptt-90) cc_final: 0.7307 (ttp80) REVERT: E 365 PRO cc_start: 0.7634 (Cg_endo) cc_final: 0.7312 (Cg_exo) REVERT: E 433 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.5329 (mt-10) REVERT: E 478 GLU cc_start: 0.6924 (tp30) cc_final: 0.6522 (pp20) REVERT: E 536 GLU cc_start: 0.6449 (tm-30) cc_final: 0.5925 (mp0) REVERT: F 160 ASP cc_start: 0.6395 (t70) cc_final: 0.5984 (t0) REVERT: F 230 MET cc_start: 0.6246 (mmt) cc_final: 0.5941 (tmm) REVERT: F 312 MET cc_start: 0.6981 (tpp) cc_final: 0.6387 (mmm) REVERT: F 433 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6058 (mt-10) REVERT: F 579 ASN cc_start: 0.7129 (t0) cc_final: 0.6835 (t0) REVERT: G 160 ASP cc_start: 0.6490 (t70) cc_final: 0.5998 (t70) REVERT: G 407 MET cc_start: 0.4318 (tmm) cc_final: 0.4034 (tmm) REVERT: G 433 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6661 (mt-10) REVERT: G 579 ASN cc_start: 0.7490 (t0) cc_final: 0.7187 (t0) REVERT: H 100 MET cc_start: 0.1202 (ttt) cc_final: -0.0449 (mtp) REVERT: H 238 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.4996 (tp) REVERT: H 316 GLU cc_start: 0.7984 (tt0) cc_final: 0.7570 (tm-30) REVERT: H 433 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5993 (mt-10) REVERT: H 579 ASN cc_start: 0.6928 (t0) cc_final: 0.6472 (t0) REVERT: H 591 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8436 (tp) REVERT: I 158 ARG cc_start: 0.2894 (OUTLIER) cc_final: 0.1625 (mmt180) REVERT: I 433 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6348 (mt-10) REVERT: J 238 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5786 (tp) REVERT: J 407 MET cc_start: 0.3608 (tmm) cc_final: 0.3301 (tmm) REVERT: J 433 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6669 (mt-10) REVERT: J 481 SER cc_start: 0.5397 (m) cc_final: 0.5012 (p) REVERT: J 536 GLU cc_start: 0.6387 (tm-30) cc_final: 0.5947 (mp0) REVERT: J 537 GLU cc_start: 0.5135 (mt-10) cc_final: 0.4524 (mt-10) REVERT: K 238 LEU cc_start: 0.4869 (pp) cc_final: 0.4612 (tp) REVERT: K 312 MET cc_start: 0.7306 (tpp) cc_final: 0.6851 (mmm) REVERT: K 316 GLU cc_start: 0.7892 (tt0) cc_final: 0.7472 (tm-30) REVERT: K 407 MET cc_start: 0.3011 (tmm) cc_final: 0.2737 (tmm) REVERT: K 579 ASN cc_start: 0.7092 (t0) cc_final: 0.6755 (t0) REVERT: L 172 LEU cc_start: 0.5167 (OUTLIER) cc_final: 0.4915 (mp) REVERT: L 251 TYR cc_start: 0.5114 (m-80) cc_final: 0.4851 (m-80) REVERT: L 407 MET cc_start: 0.3141 (tmm) cc_final: 0.2765 (tmm) REVERT: L 433 GLU cc_start: 0.6525 (mt-10) cc_final: 0.6252 (mm-30) REVERT: L 463 ARG cc_start: 0.3050 (OUTLIER) cc_final: 0.2657 (mtp85) REVERT: L 579 ASN cc_start: 0.7292 (m-40) cc_final: 0.6931 (t0) REVERT: M 251 TYR cc_start: 0.5232 (m-80) cc_final: 0.5010 (m-80) REVERT: M 407 MET cc_start: 0.1983 (OUTLIER) cc_final: 0.1570 (tmm) REVERT: M 433 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6224 (mt-10) REVERT: N 211 ARG cc_start: 0.5909 (mtt180) cc_final: 0.5290 (ptm-80) REVERT: N 251 TYR cc_start: 0.5560 (m-80) cc_final: 0.5264 (m-80) REVERT: N 312 MET cc_start: 0.7660 (tpp) cc_final: 0.7276 (mmm) REVERT: N 429 MET cc_start: 0.5713 (mmm) cc_final: 0.5455 (mmm) REVERT: N 579 ASN cc_start: 0.7573 (t0) cc_final: 0.7184 (t0) REVERT: O 251 TYR cc_start: 0.4937 (m-80) cc_final: 0.4650 (m-80) REVERT: O 312 MET cc_start: 0.7527 (tpp) cc_final: 0.7166 (mmm) REVERT: O 376 ASP cc_start: 0.5797 (m-30) cc_final: 0.5511 (p0) REVERT: O 407 MET cc_start: 0.2217 (ttp) cc_final: 0.1961 (tmm) REVERT: O 429 MET cc_start: 0.5798 (mmm) cc_final: 0.5528 (mmm) REVERT: O 433 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.6034 (mt-10) outliers start: 185 outliers final: 147 residues processed: 765 average time/residue: 0.5031 time to fit residues: 668.6354 Evaluate side-chains 768 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 601 time to evaluate : 4.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 349 GLN Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 591 LEU Chi-restraints excluded: chain I residue 158 ARG Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 531 ASP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 463 ARG Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 533 GLN Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 335 ILE Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain N residue 306 THR Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 445 GLN Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 573 THR Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 453 optimal weight: 0.9990 chunk 608 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 526 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 572 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 chunk 587 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 ASN ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 533 GLN ** N 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.221793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.207093 restraints weight = 67909.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.205944 restraints weight = 120858.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.204212 restraints weight = 63855.784| |-----------------------------------------------------------------------------| r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.6846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 55485 Z= 0.316 Angle : 0.764 11.814 75255 Z= 0.381 Chirality : 0.049 0.360 9120 Planarity : 0.005 0.095 9855 Dihedral : 5.714 43.697 7786 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.17 % Favored : 91.57 % Rotamer: Outliers : 3.23 % Allowed : 24.80 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -1.84 (0.10), residues: 7200 helix: 0.50 (0.11), residues: 2070 sheet: -1.44 (0.11), residues: 2460 loop : -2.28 (0.11), residues: 2670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 350 HIS 0.006 0.001 HIS G 133 PHE 0.027 0.002 PHE G 393 TYR 0.025 0.003 TYR L 174 ARG 0.009 0.001 ARG D 182 =============================================================================== Job complete usr+sys time: 13214.40 seconds wall clock time: 239 minutes 9.74 seconds (14349.74 seconds total)