Starting phenix.real_space_refine (version: dev) on Wed Feb 22 12:29:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/02_2023/6i1y_0327_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/02_2023/6i1y_0327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/02_2023/6i1y_0327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/02_2023/6i1y_0327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/02_2023/6i1y_0327_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1y_0327/02_2023/6i1y_0327_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 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 Process input model Symmetric amino acids flipped Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 604": "NH1" <-> "NH2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "D TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "E TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 604": "NH1" <-> "NH2" Residue "F TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 604": "NH1" <-> "NH2" Residue "G TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 604": "NH1" <-> "NH2" Residue "H TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 604": "NH1" <-> "NH2" Residue "I TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 604": "NH1" <-> "NH2" Residue "J TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 604": "NH1" <-> "NH2" Residue "K TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 604": "NH1" <-> "NH2" Residue "L TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 604": "NH1" <-> "NH2" Residue "M TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 604": "NH1" <-> "NH2" Residue "N TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 604": "NH1" <-> "NH2" Residue "O TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 604": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 56520 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "B" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "C" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "D" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "E" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "F" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "G" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "H" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "I" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "J" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "K" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "L" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "M" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "N" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Chain: "O" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3768 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 4 Time building chain proxies: 22.63, per 1000 atoms: 0.40 Number of scatterers: 56520 At special positions: 0 Unit cell: (176.66, 177.87, 192.39, 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 195 16.00 O 11040 8.00 N 9960 7.00 C 35325 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.96 Conformation dependent library (CDL) restraints added in 6.5 seconds 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13770 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 0 sheets defined 34.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 125 removed outlier: 3.830A pdb=" N ALA A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.738A pdb=" N LEU A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 311 Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.547A pdb=" N ILE A 558 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 588 through 613 removed outlier: 3.603A pdb=" N ALA A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.975A pdb=" N ILE A 623 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 649 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 114 through 125 removed outlier: 3.833A pdb=" N ALA B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 217 through 231 removed outlier: 3.741A pdb=" N LEU B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 5.035A pdb=" N ASP B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 311 Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE B 558 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 588 through 613 removed outlier: 3.605A pdb=" N ALA B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.973A pdb=" N ILE B 623 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 649 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 125 removed outlier: 3.832A pdb=" N ALA C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 160 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 217 through 231 removed outlier: 3.741A pdb=" N LEU C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 311 Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'C' and resid 397 through 404 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 554 through 558 removed outlier: 3.549A pdb=" N ILE C 558 " --> pdb=" O LEU C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 565 Processing helix chain 'C' and resid 588 through 613 removed outlier: 3.608A pdb=" N ALA C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.979A pdb=" N ILE C 623 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 649 Processing helix chain 'D' and resid 110 through 113 Processing helix chain 'D' and resid 114 through 125 removed outlier: 3.832A pdb=" N ALA D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 217 through 231 removed outlier: 3.739A pdb=" N LEU D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 311 Processing helix chain 'D' and resid 358 through 369 Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 554 through 558 removed outlier: 3.548A pdb=" N ILE D 558 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 565 Processing helix chain 'D' and resid 588 through 613 removed outlier: 3.606A pdb=" N ALA D 592 " --> pdb=" O ASP D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 623 removed outlier: 3.976A pdb=" N ILE D 623 " --> pdb=" O ASP D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 649 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 125 removed outlier: 3.833A pdb=" N ALA E 125 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 160 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 175 through 185 Processing helix chain 'E' and resid 217 through 231 removed outlier: 3.741A pdb=" N LEU E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 267 removed outlier: 5.035A pdb=" N ASP E 256 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 257 " --> pdb=" O ASP E 253 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL E 261 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 311 Processing helix chain 'E' and resid 358 through 369 Processing helix chain 'E' and resid 397 through 404 Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 554 through 558 removed outlier: 3.549A pdb=" N ILE E 558 " --> pdb=" O LEU E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 565 Processing helix chain 'E' and resid 588 through 613 removed outlier: 3.604A pdb=" N ALA E 592 " --> pdb=" O ASP E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 623 removed outlier: 3.974A pdb=" N ILE E 623 " --> pdb=" O ASP E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 649 Processing helix chain 'F' and resid 110 through 113 Processing helix chain 'F' and resid 114 through 125 removed outlier: 3.833A pdb=" N ALA F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 217 through 231 removed outlier: 3.742A pdb=" N LEU F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 267 removed outlier: 5.036A pdb=" N ASP F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 257 " --> pdb=" O ASP F 253 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN F 264 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 311 Processing helix chain 'F' and resid 358 through 369 Processing helix chain 'F' and resid 397 through 404 Processing helix chain 'F' and resid 405 through 407 No H-bonds generated for 'chain 'F' and resid 405 through 407' Processing helix chain 'F' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE F 558 " --> pdb=" O LEU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 565 Processing helix chain 'F' and resid 588 through 613 removed outlier: 3.606A pdb=" N ALA F 592 " --> pdb=" O ASP F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 623 removed outlier: 3.979A pdb=" N ILE F 623 " --> pdb=" O ASP F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 649 Processing helix chain 'G' and resid 110 through 113 Processing helix chain 'G' and resid 114 through 125 removed outlier: 3.832A pdb=" N ALA G 125 " --> pdb=" O LEU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 Processing helix chain 'G' and resid 161 through 163 No H-bonds generated for 'chain 'G' and resid 161 through 163' Processing helix chain 'G' and resid 175 through 185 Processing helix chain 'G' and resid 217 through 231 removed outlier: 3.742A pdb=" N LEU G 231 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 267 removed outlier: 5.032A pdb=" N ASP G 256 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL G 257 " --> pdb=" O ASP G 253 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL G 261 " --> pdb=" O VAL G 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 311 Processing helix chain 'G' and resid 358 through 369 Processing helix chain 'G' and resid 397 through 404 Processing helix chain 'G' and resid 405 through 407 No H-bonds generated for 'chain 'G' and resid 405 through 407' Processing helix chain 'G' and resid 554 through 558 removed outlier: 3.551A pdb=" N ILE G 558 " --> pdb=" O LEU G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 561 through 565 Processing helix chain 'G' and resid 588 through 613 removed outlier: 3.608A pdb=" N ALA G 592 " --> pdb=" O ASP G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 623 removed outlier: 3.978A pdb=" N ILE G 623 " --> pdb=" O ASP G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 636 through 649 Processing helix chain 'H' and resid 110 through 113 Processing helix chain 'H' and resid 114 through 125 removed outlier: 3.831A pdb=" N ALA H 125 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 175 through 185 Processing helix chain 'H' and resid 217 through 231 removed outlier: 3.740A pdb=" N LEU H 231 " --> pdb=" O LEU H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP H 256 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL H 257 " --> pdb=" O ASP H 253 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL H 261 " --> pdb=" O VAL H 257 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN H 264 " --> pdb=" O GLY H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 311 Processing helix chain 'H' and resid 358 through 369 Processing helix chain 'H' and resid 397 through 404 Processing helix chain 'H' and resid 405 through 407 No H-bonds generated for 'chain 'H' and resid 405 through 407' Processing helix chain 'H' and resid 554 through 558 removed outlier: 3.548A pdb=" N ILE H 558 " --> pdb=" O LEU H 555 " (cutoff:3.500A) Processing helix chain 'H' and resid 561 through 565 Processing helix chain 'H' and resid 588 through 613 removed outlier: 3.605A pdb=" N ALA H 592 " --> pdb=" O ASP H 588 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 623 removed outlier: 3.976A pdb=" N ILE H 623 " --> pdb=" O ASP H 620 " (cutoff:3.500A) Processing helix chain 'H' and resid 636 through 649 Processing helix chain 'I' and resid 110 through 113 Processing helix chain 'I' and resid 114 through 125 removed outlier: 3.832A pdb=" N ALA I 125 " --> pdb=" O LEU I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 160 Processing helix chain 'I' and resid 161 through 163 No H-bonds generated for 'chain 'I' and resid 161 through 163' Processing helix chain 'I' and resid 175 through 185 Processing helix chain 'I' and resid 217 through 231 removed outlier: 3.741A pdb=" N LEU I 231 " --> pdb=" O LEU I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP I 256 " --> pdb=" O GLU I 252 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL I 257 " --> pdb=" O ASP I 253 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY I 260 " --> pdb=" O ASP I 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL I 261 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 311 Processing helix chain 'I' and resid 358 through 369 Processing helix chain 'I' and resid 397 through 404 Processing helix chain 'I' and resid 405 through 407 No H-bonds generated for 'chain 'I' and resid 405 through 407' Processing helix chain 'I' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE I 558 " --> pdb=" O LEU I 555 " (cutoff:3.500A) Processing helix chain 'I' and resid 561 through 565 Processing helix chain 'I' and resid 588 through 613 removed outlier: 3.606A pdb=" N ALA I 592 " --> pdb=" O ASP I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 623 removed outlier: 3.974A pdb=" N ILE I 623 " --> pdb=" O ASP I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 636 through 649 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 125 removed outlier: 3.831A pdb=" N ALA J 125 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 160 Processing helix chain 'J' and resid 161 through 163 No H-bonds generated for 'chain 'J' and resid 161 through 163' Processing helix chain 'J' and resid 175 through 185 Processing helix chain 'J' and resid 217 through 231 removed outlier: 3.740A pdb=" N LEU J 231 " --> pdb=" O LEU J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP J 256 " --> pdb=" O GLU J 252 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL J 257 " --> pdb=" O ASP J 253 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY J 260 " --> pdb=" O ASP J 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL J 261 " --> pdb=" O VAL J 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 299 through 311 Processing helix chain 'J' and resid 358 through 369 Processing helix chain 'J' and resid 397 through 404 Processing helix chain 'J' and resid 405 through 407 No H-bonds generated for 'chain 'J' and resid 405 through 407' Processing helix chain 'J' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE J 558 " --> pdb=" O LEU J 555 " (cutoff:3.500A) Processing helix chain 'J' and resid 561 through 565 Processing helix chain 'J' and resid 588 through 613 removed outlier: 3.606A pdb=" N ALA J 592 " --> pdb=" O ASP J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 623 removed outlier: 3.979A pdb=" N ILE J 623 " --> pdb=" O ASP J 620 " (cutoff:3.500A) Processing helix chain 'J' and resid 636 through 649 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 125 removed outlier: 3.831A pdb=" N ALA K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 160 Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'K' and resid 175 through 185 Processing helix chain 'K' and resid 217 through 231 removed outlier: 3.739A pdb=" N LEU K 231 " --> pdb=" O LEU K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 267 removed outlier: 5.033A pdb=" N ASP K 256 " --> pdb=" O GLU K 252 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL K 257 " --> pdb=" O ASP K 253 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY K 260 " --> pdb=" O ASP K 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL K 261 " --> pdb=" O VAL K 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN K 264 " --> pdb=" O GLY K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 311 Processing helix chain 'K' and resid 358 through 369 Processing helix chain 'K' and resid 397 through 404 Processing helix chain 'K' and resid 405 through 407 No H-bonds generated for 'chain 'K' and resid 405 through 407' Processing helix chain 'K' and resid 554 through 558 removed outlier: 3.548A pdb=" N ILE K 558 " --> pdb=" O LEU K 555 " (cutoff:3.500A) Processing helix chain 'K' and resid 561 through 565 Processing helix chain 'K' and resid 588 through 613 removed outlier: 3.608A pdb=" N ALA K 592 " --> pdb=" O ASP K 588 " (cutoff:3.500A) Processing helix chain 'K' and resid 619 through 623 removed outlier: 3.981A pdb=" N ILE K 623 " --> pdb=" O ASP K 620 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 649 Processing helix chain 'L' and resid 110 through 113 Processing helix chain 'L' and resid 114 through 125 removed outlier: 3.832A pdb=" N ALA L 125 " --> pdb=" O LEU L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 160 Processing helix chain 'L' and resid 161 through 163 No H-bonds generated for 'chain 'L' and resid 161 through 163' Processing helix chain 'L' and resid 175 through 185 Processing helix chain 'L' and resid 217 through 231 removed outlier: 3.740A pdb=" N LEU L 231 " --> pdb=" O LEU L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 267 removed outlier: 5.030A pdb=" N ASP L 256 " --> pdb=" O GLU L 252 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL L 257 " --> pdb=" O ASP L 253 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY L 260 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL L 261 " --> pdb=" O VAL L 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN L 264 " --> pdb=" O GLY L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 311 Processing helix chain 'L' and resid 358 through 369 Processing helix chain 'L' and resid 397 through 404 Processing helix chain 'L' and resid 405 through 407 No H-bonds generated for 'chain 'L' and resid 405 through 407' Processing helix chain 'L' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE L 558 " --> pdb=" O LEU L 555 " (cutoff:3.500A) Processing helix chain 'L' and resid 561 through 565 Processing helix chain 'L' and resid 588 through 613 removed outlier: 3.605A pdb=" N ALA L 592 " --> pdb=" O ASP L 588 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 623 removed outlier: 3.974A pdb=" N ILE L 623 " --> pdb=" O ASP L 620 " (cutoff:3.500A) Processing helix chain 'L' and resid 636 through 649 Processing helix chain 'M' and resid 110 through 113 Processing helix chain 'M' and resid 114 through 125 removed outlier: 3.833A pdb=" N ALA M 125 " --> pdb=" O LEU M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 160 Processing helix chain 'M' and resid 161 through 163 No H-bonds generated for 'chain 'M' and resid 161 through 163' Processing helix chain 'M' and resid 175 through 185 Processing helix chain 'M' and resid 217 through 231 removed outlier: 3.740A pdb=" N LEU M 231 " --> pdb=" O LEU M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 267 removed outlier: 5.036A pdb=" N ASP M 256 " --> pdb=" O GLU M 252 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL M 257 " --> pdb=" O ASP M 253 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY M 260 " --> pdb=" O ASP M 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL M 261 " --> pdb=" O VAL M 257 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN M 264 " --> pdb=" O GLY M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 299 through 311 Processing helix chain 'M' and resid 358 through 369 Processing helix chain 'M' and resid 397 through 404 Processing helix chain 'M' and resid 405 through 407 No H-bonds generated for 'chain 'M' and resid 405 through 407' Processing helix chain 'M' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE M 558 " --> pdb=" O LEU M 555 " (cutoff:3.500A) Processing helix chain 'M' and resid 561 through 565 Processing helix chain 'M' and resid 588 through 613 removed outlier: 3.606A pdb=" N ALA M 592 " --> pdb=" O ASP M 588 " (cutoff:3.500A) Processing helix chain 'M' and resid 619 through 623 removed outlier: 3.975A pdb=" N ILE M 623 " --> pdb=" O ASP M 620 " (cutoff:3.500A) Processing helix chain 'M' and resid 636 through 649 Processing helix chain 'N' and resid 110 through 113 Processing helix chain 'N' and resid 114 through 125 removed outlier: 3.831A pdb=" N ALA N 125 " --> pdb=" O LEU N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 160 Processing helix chain 'N' and resid 161 through 163 No H-bonds generated for 'chain 'N' and resid 161 through 163' Processing helix chain 'N' and resid 175 through 185 Processing helix chain 'N' and resid 217 through 231 removed outlier: 3.742A pdb=" N LEU N 231 " --> pdb=" O LEU N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 267 removed outlier: 5.035A pdb=" N ASP N 256 " --> pdb=" O GLU N 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL N 257 " --> pdb=" O ASP N 253 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY N 260 " --> pdb=" O ASP N 256 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL N 261 " --> pdb=" O VAL N 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN N 264 " --> pdb=" O GLY N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 311 Processing helix chain 'N' and resid 358 through 369 Processing helix chain 'N' and resid 397 through 404 Processing helix chain 'N' and resid 405 through 407 No H-bonds generated for 'chain 'N' and resid 405 through 407' Processing helix chain 'N' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE N 558 " --> pdb=" O LEU N 555 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 565 Processing helix chain 'N' and resid 588 through 613 removed outlier: 3.606A pdb=" N ALA N 592 " --> pdb=" O ASP N 588 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 623 removed outlier: 3.979A pdb=" N ILE N 623 " --> pdb=" O ASP N 620 " (cutoff:3.500A) Processing helix chain 'N' and resid 636 through 649 Processing helix chain 'O' and resid 110 through 113 Processing helix chain 'O' and resid 114 through 125 removed outlier: 3.831A pdb=" N ALA O 125 " --> pdb=" O LEU O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 160 Processing helix chain 'O' and resid 161 through 163 No H-bonds generated for 'chain 'O' and resid 161 through 163' Processing helix chain 'O' and resid 175 through 185 Processing helix chain 'O' and resid 217 through 231 removed outlier: 3.741A pdb=" N LEU O 231 " --> pdb=" O LEU O 227 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 267 removed outlier: 5.032A pdb=" N ASP O 256 " --> pdb=" O GLU O 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL O 257 " --> pdb=" O ASP O 253 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY O 260 " --> pdb=" O ASP O 256 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL O 261 " --> pdb=" O VAL O 257 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN O 264 " --> pdb=" O GLY O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 311 Processing helix chain 'O' and resid 358 through 369 Processing helix chain 'O' and resid 397 through 404 Processing helix chain 'O' and resid 405 through 407 No H-bonds generated for 'chain 'O' and resid 405 through 407' Processing helix chain 'O' and resid 554 through 558 removed outlier: 3.550A pdb=" N ILE O 558 " --> pdb=" O LEU O 555 " (cutoff:3.500A) Processing helix chain 'O' and resid 561 through 565 Processing helix chain 'O' and resid 588 through 613 removed outlier: 3.607A pdb=" N ALA O 592 " --> pdb=" O ASP O 588 " (cutoff:3.500A) Processing helix chain 'O' and resid 619 through 623 removed outlier: 3.976A pdb=" N ILE O 623 " --> pdb=" O ASP O 620 " (cutoff:3.500A) Processing helix chain 'O' and resid 636 through 649 1530 hydrogen bonds defined for protein. 4365 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: 11.66 Time building geometry restraints manager: 18.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 10390 1.30 - 1.44: 11923 1.44 - 1.57: 34312 1.57 - 1.70: 0 1.70 - 1.83: 390 Bond restraints: 57015 Sorted by residual: bond pdb=" C ASN N 524 " pdb=" O ASN N 524 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.14e-02 7.69e+03 3.36e+01 bond pdb=" C ASN E 524 " pdb=" O ASN E 524 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.14e-02 7.69e+03 3.30e+01 bond pdb=" C ASN M 524 " pdb=" O ASN M 524 " ideal model delta sigma weight residual 1.236 1.170 0.065 1.14e-02 7.69e+03 3.29e+01 bond pdb=" C ASN F 524 " pdb=" O ASN F 524 " ideal model delta sigma weight residual 1.236 1.171 0.065 1.14e-02 7.69e+03 3.28e+01 bond pdb=" C ASN G 524 " pdb=" O ASN G 524 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.19e-02 7.06e+03 3.10e+01 ... (remaining 57010 not shown) Histogram of bond angle deviations from ideal: 97.14 - 104.57: 995 104.57 - 111.99: 26432 111.99 - 119.42: 27738 119.42 - 126.85: 21609 126.85 - 134.27: 401 Bond angle restraints: 77175 Sorted by residual: angle pdb=" C GLU N 503 " pdb=" N VAL N 504 " pdb=" CA VAL N 504 " ideal model delta sigma weight residual 122.91 109.11 13.80 1.43e+00 4.89e-01 9.31e+01 angle pdb=" C GLU C 503 " pdb=" N VAL C 504 " pdb=" CA VAL C 504 " ideal model delta sigma weight residual 122.91 109.13 13.78 1.43e+00 4.89e-01 9.29e+01 angle pdb=" C GLU J 503 " pdb=" N VAL J 504 " pdb=" CA VAL J 504 " ideal model delta sigma weight residual 122.91 109.17 13.74 1.43e+00 4.89e-01 9.24e+01 angle pdb=" C GLU G 503 " pdb=" N VAL G 504 " pdb=" CA VAL G 504 " ideal model delta sigma weight residual 122.91 109.18 13.73 1.43e+00 4.89e-01 9.22e+01 angle pdb=" C GLU F 503 " pdb=" N VAL F 504 " pdb=" CA VAL F 504 " ideal model delta sigma weight residual 122.91 109.21 13.70 1.43e+00 4.89e-01 9.18e+01 ... (remaining 77170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 30832 14.38 - 28.76: 3414 28.76 - 43.13: 831 43.13 - 57.51: 128 57.51 - 71.89: 60 Dihedral angle restraints: 35265 sinusoidal: 14010 harmonic: 21255 Sorted by residual: dihedral pdb=" CA ALA A 298 " pdb=" C ALA A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta harmonic sigma weight residual 180.00 139.69 40.31 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA ALA E 298 " pdb=" C ALA E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta harmonic sigma weight residual 180.00 139.73 40.27 0 5.00e+00 4.00e-02 6.49e+01 dihedral pdb=" CA ALA C 298 " pdb=" C ALA C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta harmonic sigma weight residual 180.00 139.73 40.27 0 5.00e+00 4.00e-02 6.49e+01 ... (remaining 35262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4193 0.069 - 0.137: 3655 0.137 - 0.206: 1302 0.206 - 0.275: 241 0.275 - 0.343: 29 Chirality restraints: 9420 Sorted by residual: chirality pdb=" CA ASP G 531 " pdb=" N ASP G 531 " pdb=" C ASP G 531 " pdb=" CB ASP G 531 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASP E 531 " pdb=" N ASP E 531 " pdb=" C ASP E 531 " pdb=" CB ASP E 531 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASP L 531 " pdb=" N ASP L 531 " pdb=" C ASP L 531 " pdb=" CB ASP L 531 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 9417 not shown) Planarity restraints: 10065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 565 " -0.082 2.00e-02 2.50e+03 7.58e-02 1.01e+02 pdb=" CG PHE J 565 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE J 565 " 0.130 2.00e-02 2.50e+03 pdb=" CD2 PHE J 565 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE J 565 " -0.087 2.00e-02 2.50e+03 pdb=" CE2 PHE J 565 " 0.058 2.00e-02 2.50e+03 pdb=" CZ PHE J 565 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 565 " -0.075 2.00e-02 2.50e+03 7.51e-02 9.88e+01 pdb=" CG PHE F 565 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE F 565 " 0.128 2.00e-02 2.50e+03 pdb=" CD2 PHE F 565 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE F 565 " -0.087 2.00e-02 2.50e+03 pdb=" CE2 PHE F 565 " 0.066 2.00e-02 2.50e+03 pdb=" CZ PHE F 565 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 565 " -0.068 2.00e-02 2.50e+03 7.42e-02 9.63e+01 pdb=" CG PHE H 565 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE H 565 " 0.128 2.00e-02 2.50e+03 pdb=" CD2 PHE H 565 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE H 565 " -0.087 2.00e-02 2.50e+03 pdb=" CE2 PHE H 565 " 0.071 2.00e-02 2.50e+03 pdb=" CZ PHE H 565 " -0.049 2.00e-02 2.50e+03 ... (remaining 10062 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 150 2.02 - 2.74: 8015 2.74 - 3.46: 85586 3.46 - 4.18: 140918 4.18 - 4.90: 244311 Nonbonded interactions: 478980 Sorted by model distance: nonbonded pdb=" O GLN H 312 " pdb=" OH TYR I 245 " model vdw 1.301 2.440 nonbonded pdb=" O GLN K 312 " pdb=" OH TYR L 245 " model vdw 1.302 2.440 nonbonded pdb=" O GLN D 312 " pdb=" OH TYR E 245 " model vdw 1.304 2.440 nonbonded pdb=" OH TYR A 245 " pdb=" O GLN O 312 " model vdw 1.306 2.440 nonbonded pdb=" O GLN A 312 " pdb=" OH TYR B 245 " model vdw 1.307 2.440 ... (remaining 478975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 35325 2.51 5 N 9960 2.21 5 O 11040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.030 Extract box with map and model: 6.970 Check model and map are aligned: 0.640 Process input model: 98.720 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Set scattering table: 0.390 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:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.015 0.093 57015 Z= 0.968 Angle : 2.010 13.799 77175 Z= 1.399 Chirality : 0.100 0.343 9420 Planarity : 0.023 0.123 10065 Dihedral : 13.306 71.888 21495 Min Nonbonded Distance : 1.301 Molprobity Statistics. All-atom Clashscore : 75.50 Ramachandran Plot: Outliers : 3.29 % Allowed : 10.91 % Favored : 85.80 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.84 % 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: -5.20 (0.08), residues: 7290 helix: -3.58 (0.08), residues: 2070 sheet: -3.21 (0.08), residues: 2895 loop : -3.04 (0.09), residues: 2325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1376 time to evaluate : 4.930 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 outliers start: 45 outliers final: 18 residues processed: 1391 average time/residue: 0.5659 time to fit residues: 1291.2458 Evaluate side-chains 819 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 801 time to evaluate : 4.979 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4626 time to fit residues: 21.6864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 620 optimal weight: 1.9990 chunk 557 optimal weight: 0.9980 chunk 309 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 375 optimal weight: 0.5980 chunk 297 optimal weight: 8.9990 chunk 576 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 350 optimal weight: 2.9990 chunk 428 optimal weight: 0.7980 chunk 667 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS D 241 ASN ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 GLN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 241 ASN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 GLN E 408 ASN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS F 241 ASN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 ASN ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 241 ASN ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 HIS G 307 GLN ** G 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 ASN H 289 GLN ** H 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN H 635 HIS I 132 HIS I 241 ASN ** I 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS J 241 ASN ** J 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 408 ASN ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 524 ASN J 635 HIS K 241 ASN ** K 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 GLN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 HIS ** L 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 635 HIS M 132 HIS M 241 ASN ** M 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 408 ASN ** M 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 635 HIS N 241 ASN ** N 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 GLN ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 241 ASN ** O 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN O 635 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 57015 Z= 0.276 Angle : 0.737 8.769 77175 Z= 0.380 Chirality : 0.049 0.214 9420 Planarity : 0.006 0.104 10065 Dihedral : 5.938 22.509 7875 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.95 % Favored : 93.84 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.09), residues: 7290 helix: -1.35 (0.10), residues: 2280 sheet: -2.57 (0.09), residues: 2580 loop : -2.28 (0.11), residues: 2430 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1089 time to evaluate : 5.024 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 outliers start: 152 outliers final: 36 residues processed: 1171 average time/residue: 0.5143 time to fit residues: 1036.3316 Evaluate side-chains 876 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 840 time to evaluate : 5.664 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4327 time to fit residues: 36.1485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 555 optimal weight: 3.9990 chunk 454 optimal weight: 5.9990 chunk 184 optimal weight: 0.4980 chunk 668 optimal weight: 0.0030 chunk 722 optimal weight: 4.9990 chunk 595 optimal weight: 20.0000 chunk 663 optimal weight: 0.7980 chunk 227 optimal weight: 0.8980 chunk 536 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 288 HIS B 312 GLN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN C 264 ASN ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 ASN C 502 GLN ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 312 GLN D 408 ASN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN E 264 ASN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 GLN E 533 GLN F 264 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 HIS ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 502 GLN F 522 GLN F 533 GLN G 264 ASN ** G 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 ASN G 502 GLN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 408 ASN H 502 GLN I 264 ASN I 288 HIS I 307 GLN ** I 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 445 ASN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 264 ASN J 289 GLN ** J 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 502 GLN ** K 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 HIS ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 408 ASN K 502 GLN ** L 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 HIS ** L 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 264 ASN M 288 HIS ** M 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 502 GLN M 524 ASN N 264 ASN ** N 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 408 ASN ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 533 GLN O 264 ASN ** O 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 288 HIS ** O 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 502 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 57015 Z= 0.207 Angle : 0.617 7.560 77175 Z= 0.313 Chirality : 0.047 0.206 9420 Planarity : 0.005 0.101 10065 Dihedral : 4.947 19.320 7875 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.53 % Favored : 95.27 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.09), residues: 7290 helix: -0.48 (0.10), residues: 2355 sheet: -2.27 (0.09), residues: 2715 loop : -1.91 (0.12), residues: 2220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 903 time to evaluate : 6.244 Fit side-chains revert: symmetry clash outliers start: 149 outliers final: 52 residues processed: 1013 average time/residue: 0.5312 time to fit residues: 928.1764 Evaluate side-chains 788 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 736 time to evaluate : 4.995 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.4160 time to fit residues: 47.5806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 7.9990 chunk 502 optimal weight: 20.0000 chunk 347 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 319 optimal weight: 5.9990 chunk 449 optimal weight: 8.9990 chunk 671 optimal weight: 2.9990 chunk 710 optimal weight: 9.9990 chunk 350 optimal weight: 0.9990 chunk 636 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 HIS ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN D 288 HIS D 502 GLN E 288 HIS E 408 ASN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN F 533 GLN G 408 ASN H 288 HIS H 312 GLN H 601 ASN I 312 GLN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 522 GLN ** J 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 HIS J 408 ASN J 533 GLN K 264 ASN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 264 ASN L 319 GLN L 408 ASN ** L 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 307 GLN M 522 GLN N 288 HIS N 312 GLN ** N 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 601 ASN O 522 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.076 57015 Z= 0.522 Angle : 0.750 8.490 77175 Z= 0.379 Chirality : 0.049 0.221 9420 Planarity : 0.006 0.097 10065 Dihedral : 5.327 21.384 7875 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.00 % Favored : 90.80 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.09), residues: 7290 helix: -0.34 (0.11), residues: 2340 sheet: -2.21 (0.09), residues: 2685 loop : -1.91 (0.12), residues: 2265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 736 time to evaluate : 5.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 272 outliers final: 122 residues processed: 956 average time/residue: 0.5154 time to fit residues: 851.7518 Evaluate side-chains 774 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 652 time to evaluate : 5.016 Switching outliers to nearest non-outliers outliers start: 122 outliers final: 0 residues processed: 122 average time/residue: 0.4099 time to fit residues: 100.7589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 40.0000 chunk 403 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 528 optimal weight: 0.9990 chunk 293 optimal weight: 4.9990 chunk 606 optimal weight: 1.9990 chunk 491 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 362 optimal weight: 4.9990 chunk 637 optimal weight: 10.0000 chunk 179 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 522 GLN B 241 ASN C 533 GLN E 524 ASN ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 GLN F 312 GLN G 266 GLN G 408 ASN G 489 GLN H 408 ASN ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 57015 Z= 0.337 Angle : 0.639 8.408 77175 Z= 0.323 Chirality : 0.047 0.208 9420 Planarity : 0.006 0.094 10065 Dihedral : 4.992 21.755 7875 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.17 % Favored : 93.62 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.09), residues: 7290 helix: -0.04 (0.11), residues: 2310 sheet: -2.28 (0.09), residues: 2760 loop : -1.78 (0.12), residues: 2220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 732 time to evaluate : 5.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 179 outliers final: 73 residues processed: 871 average time/residue: 0.5278 time to fit residues: 796.0896 Evaluate side-chains 726 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 653 time to evaluate : 5.057 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.4102 time to fit residues: 64.1040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 2.9990 chunk 639 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 417 optimal weight: 0.2980 chunk 175 optimal weight: 10.0000 chunk 711 optimal weight: 9.9990 chunk 590 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 373 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 132 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN E 240 ASN E 524 ASN G 266 GLN I 132 HIS ** I 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 ASN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 266 GLN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN L 502 GLN ** N 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 489 GLN N 502 GLN N 506 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 57015 Z= 0.268 Angle : 0.607 8.281 77175 Z= 0.308 Chirality : 0.046 0.204 9420 Planarity : 0.005 0.091 10065 Dihedral : 4.747 20.169 7875 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.04 % Favored : 92.76 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.10), residues: 7290 helix: 0.17 (0.11), residues: 2310 sheet: -2.22 (0.09), residues: 2730 loop : -1.60 (0.12), residues: 2250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 710 time to evaluate : 5.224 Fit side-chains revert: symmetry clash outliers start: 107 outliers final: 43 residues processed: 784 average time/residue: 0.5213 time to fit residues: 703.7182 Evaluate side-chains 695 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 652 time to evaluate : 4.956 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4139 time to fit residues: 40.2947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 405 optimal weight: 0.5980 chunk 519 optimal weight: 7.9990 chunk 402 optimal weight: 5.9990 chunk 598 optimal weight: 7.9990 chunk 397 optimal weight: 5.9990 chunk 708 optimal weight: 7.9990 chunk 443 optimal weight: 9.9990 chunk 431 optimal weight: 8.9990 chunk 327 optimal weight: 2.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN G 408 ASN ** G 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 266 GLN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 GLN ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 266 GLN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 57015 Z= 0.411 Angle : 0.674 9.182 77175 Z= 0.342 Chirality : 0.047 0.212 9420 Planarity : 0.006 0.090 10065 Dihedral : 4.999 21.547 7875 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.52 % Favored : 91.28 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.10), residues: 7290 helix: 0.07 (0.11), residues: 2325 sheet: -2.38 (0.09), residues: 2955 loop : -1.46 (0.13), residues: 2010 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 680 time to evaluate : 5.079 Fit side-chains revert: symmetry clash outliers start: 120 outliers final: 58 residues processed: 762 average time/residue: 0.5269 time to fit residues: 689.4069 Evaluate side-chains 699 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 641 time to evaluate : 5.015 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4225 time to fit residues: 52.2436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 0.0980 chunk 282 optimal weight: 0.7980 chunk 423 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 450 optimal weight: 5.9990 chunk 482 optimal weight: 7.9990 chunk 350 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 556 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 HIS G 635 HIS H 266 GLN H 489 GLN H 635 HIS ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 307 GLN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 635 HIS L 408 ASN N 240 ASN N 506 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 57015 Z= 0.223 Angle : 0.596 9.398 77175 Z= 0.303 Chirality : 0.046 0.202 9420 Planarity : 0.005 0.088 10065 Dihedral : 4.675 22.596 7875 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.25 % Favored : 94.54 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.10), residues: 7290 helix: 0.28 (0.11), residues: 2325 sheet: -2.21 (0.09), residues: 2700 loop : -1.51 (0.13), residues: 2265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 695 time to evaluate : 5.043 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 22 residues processed: 736 average time/residue: 0.5402 time to fit residues: 683.3422 Evaluate side-chains 656 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 634 time to evaluate : 4.969 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4488 time to fit residues: 24.8916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 1.9990 chunk 678 optimal weight: 9.9990 chunk 619 optimal weight: 0.4980 chunk 660 optimal weight: 5.9990 chunk 397 optimal weight: 2.9990 chunk 287 optimal weight: 0.9980 chunk 518 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 596 optimal weight: 7.9990 chunk 624 optimal weight: 2.9990 chunk 657 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 ASN C 266 GLN E 524 ASN H 489 GLN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 GLN ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN M 576 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 57015 Z= 0.266 Angle : 0.616 11.957 77175 Z= 0.311 Chirality : 0.046 0.276 9420 Planarity : 0.006 0.086 10065 Dihedral : 4.644 21.760 7875 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.42 % Favored : 92.37 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.10), residues: 7290 helix: 0.36 (0.11), residues: 2310 sheet: -2.32 (0.09), residues: 2790 loop : -1.20 (0.13), residues: 2190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 655 time to evaluate : 5.348 Fit side-chains outliers start: 39 outliers final: 20 residues processed: 682 average time/residue: 0.5335 time to fit residues: 623.8393 Evaluate side-chains 649 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 629 time to evaluate : 5.054 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4030 time to fit residues: 22.3361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 9.9990 chunk 698 optimal weight: 9.9990 chunk 426 optimal weight: 0.5980 chunk 331 optimal weight: 0.0170 chunk 485 optimal weight: 3.9990 chunk 732 optimal weight: 10.0000 chunk 673 optimal weight: 3.9990 chunk 583 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 450 optimal weight: 7.9990 chunk 357 optimal weight: 0.9980 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 GLN I 307 GLN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 GLN ** J 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 502 GLN ** K 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 57015 Z= 0.202 Angle : 0.591 11.913 77175 Z= 0.300 Chirality : 0.046 0.246 9420 Planarity : 0.005 0.084 10065 Dihedral : 4.445 22.354 7875 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.84 % Favored : 94.95 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.10), residues: 7290 helix: 0.52 (0.11), residues: 2310 sheet: -2.26 (0.09), residues: 2820 loop : -1.00 (0.13), residues: 2160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 658 time to evaluate : 5.048 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 672 average time/residue: 0.5452 time to fit residues: 625.7827 Evaluate side-chains 611 residues out of total 6210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 607 time to evaluate : 4.978 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4114 time to fit residues: 9.9624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 1.9990 chunk 621 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 537 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 584 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 599 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN E 524 ASN ** I 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 GLN ** K 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.195098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.157011 restraints weight = 72371.350| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.83 r_work: 0.3735 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 57015 Z= 0.214 Angle : 0.588 13.055 77175 Z= 0.298 Chirality : 0.046 0.231 9420 Planarity : 0.005 0.083 10065 Dihedral : 4.390 21.952 7875 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.39 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.10), residues: 7290 helix: 0.62 (0.11), residues: 2310 sheet: -2.26 (0.09), residues: 2880 loop : -0.87 (0.14), residues: 2100 =============================================================================== Job complete usr+sys time: 13047.95 seconds wall clock time: 230 minutes 27.03 seconds (13827.03 seconds total)