Starting phenix.real_space_refine (version: dev) on Sun Dec 18 14:14:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7waf_32384/12_2022/7waf_32384_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7waf_32384/12_2022/7waf_32384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7waf_32384/12_2022/7waf_32384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7waf_32384/12_2022/7waf_32384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7waf_32384/12_2022/7waf_32384_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7waf_32384/12_2022/7waf_32384_updated_updated.pdb" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 168": "OE1" <-> "OE2" Residue "A PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "I ARG 101": "NH1" <-> "NH2" Residue "J ARG 101": "NH1" <-> "NH2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "L ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 24842 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 877, 6683 Classifications: {'peptide': 877} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 841} Chain: "B" Number of atoms: 6683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 877, 6683 Classifications: {'peptide': 877} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 841} Chain: "C" Number of atoms: 5510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5510 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 695} Chain: "D" Number of atoms: 5510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5510 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 695} Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'AGS': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'AGS': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'AGS': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'AGS': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "J" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "K" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Time building chain proxies: 14.52, per 1000 atoms: 0.58 Number of scatterers: 24842 At special positions: 0 Unit cell: (165.17, 163.51, 123.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 24 15.00 Mg 12 11.99 O 4788 8.00 N 4356 7.00 C 15574 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: 10.67 Conformation dependent library (CDL) restraints added in 4.2 seconds 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5812 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 118 helices and 26 sheets defined 36.7% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 119 through 139 removed outlier: 3.840A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 243 through 253 removed outlier: 4.184A pdb=" N GLN A 247 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 253 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 291 Processing helix chain 'A' and resid 336 through 344 removed outlier: 4.503A pdb=" N GLU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 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 410 through 423 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.154A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 595 through 607 removed outlier: 3.797A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 628 removed outlier: 3.572A pdb=" N MET A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 691 through 707 removed outlier: 3.673A pdb=" N GLN A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 720 Processing helix chain 'A' and resid 750 through 762 removed outlier: 3.549A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN A 762 " --> pdb=" O GLY A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 792 Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 842 through 851 Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 77 through 91 Processing helix chain 'B' and resid 119 through 139 removed outlier: 3.843A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 Processing helix chain 'B' and resid 165 through 176 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 220 through 229 Processing helix chain 'B' and resid 243 through 253 removed outlier: 4.177A pdb=" N GLN B 247 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 253 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 291 Processing helix chain 'B' and resid 336 through 344 removed outlier: 4.515A pdb=" N GLU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 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 410 through 423 Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.167A pdb=" N LEU B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 595 through 607 removed outlier: 3.798A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 628 removed outlier: 3.578A pdb=" N MET B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA B 628 " --> pdb=" O VAL B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 691 through 707 removed outlier: 3.667A pdb=" N GLN B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 720 Processing helix chain 'B' and resid 750 through 762 removed outlier: 3.552A pdb=" N PHE B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 792 Processing helix chain 'B' and resid 811 through 825 Processing helix chain 'B' and resid 842 through 851 Processing helix chain 'B' and resid 866 through 875 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 77 through 91 Processing helix chain 'C' and resid 119 through 139 removed outlier: 3.783A pdb=" N VAL C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 220 through 229 Processing helix chain 'C' and resid 246 through 253 removed outlier: 3.543A pdb=" N TYR C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 291 Processing helix chain 'C' and resid 336 through 344 removed outlier: 4.740A pdb=" N GLU C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' 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 410 through 423 Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 499 through 512 Processing helix chain 'C' and resid 540 through 547 removed outlier: 4.173A pdb=" N LEU C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 567 Processing helix chain 'C' and resid 595 through 607 removed outlier: 3.796A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 628 removed outlier: 3.626A pdb=" N MET C 627 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA C 628 " --> pdb=" O VAL C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 652 Processing helix chain 'C' and resid 683 through 685 No H-bonds generated for 'chain 'C' and resid 683 through 685' Processing helix chain 'C' and resid 691 through 707 removed outlier: 3.656A pdb=" N GLN C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 720 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 77 through 91 Processing helix chain 'D' and resid 119 through 139 removed outlier: 3.781A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 220 through 229 Processing helix chain 'D' and resid 246 through 253 removed outlier: 3.527A pdb=" N TYR D 252 " --> pdb=" O ASP D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 291 Processing helix chain 'D' and resid 336 through 344 removed outlier: 4.724A pdb=" N GLU D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 373 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' 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 410 through 423 Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 499 through 512 Processing helix chain 'D' and resid 540 through 547 removed outlier: 4.147A pdb=" N LEU D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 567 Processing helix chain 'D' and resid 595 through 607 removed outlier: 3.795A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 628 removed outlier: 3.633A pdb=" N MET D 627 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA D 628 " --> pdb=" O VAL D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 652 Processing helix chain 'D' and resid 683 through 685 No H-bonds generated for 'chain 'D' and resid 683 through 685' Processing helix chain 'D' and resid 691 through 707 removed outlier: 3.653A pdb=" N GLN D 707 " --> pdb=" O ALA D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 720 Processing sheet with id= A, first strand: chain 'A' and resid 99 through 103 removed outlier: 3.728A pdb=" N LYS A 5 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP A 28 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE A 3 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= C, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= D, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.774A pdb=" N LEU A 311 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 320 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 309 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU A 322 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP A 307 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 450 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 327 through 329 Processing sheet with id= F, first strand: chain 'A' and resid 673 through 677 removed outlier: 6.791A pdb=" N ILE A 665 " --> pdb=" O ILE A 676 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N SER A 639 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 618 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE A 527 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 733 through 736 removed outlier: 6.336A pdb=" N GLU A 795 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 771 " --> pdb=" O GLU A 795 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 797 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR A 835 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE A 798 " --> pdb=" O THR A 835 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU A 837 " --> pdb=" O ILE A 798 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 99 through 103 removed outlier: 3.727A pdb=" N LYS B 5 " --> pdb=" O ARG B 26 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP B 28 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE B 3 " --> pdb=" O ASP B 28 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= J, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= K, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.776A pdb=" N LEU B 311 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 320 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG B 309 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU B 322 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASP B 307 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 450 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 433 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE B 448 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 327 through 329 Processing sheet with id= M, first strand: chain 'B' and resid 673 through 677 removed outlier: 6.796A pdb=" N ILE B 665 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER B 639 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 618 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE B 527 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 733 through 736 removed outlier: 6.336A pdb=" N GLU B 795 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 771 " --> pdb=" O GLU B 795 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 797 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR B 835 " --> pdb=" O ILE B 796 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE B 798 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLU B 837 " --> pdb=" O ILE B 798 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 99 through 103 removed outlier: 3.795A pdb=" N LYS C 5 " --> pdb=" O ARG C 26 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE C 3 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= Q, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= R, first strand: chain 'C' and resid 400 through 403 removed outlier: 6.793A pdb=" N LEU C 311 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL C 320 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG C 309 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU C 322 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP C 307 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 450 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 327 through 329 Processing sheet with id= T, first strand: chain 'C' and resid 673 through 677 removed outlier: 6.805A pdb=" N ILE C 665 " --> pdb=" O ILE C 676 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N SER C 639 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN C 618 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE C 527 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU C 531 " --> pdb=" O ILE C 527 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 99 through 103 removed outlier: 3.783A pdb=" N LYS D 5 " --> pdb=" O ARG D 26 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP D 28 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE D 3 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= W, first strand: chain 'D' and resid 237 through 240 removed outlier: 3.521A pdb=" N VAL D 297 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 400 through 403 removed outlier: 6.791A pdb=" N LEU D 311 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL D 320 " --> pdb=" O ARG D 309 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG D 309 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU D 322 " --> pdb=" O ASP D 307 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP D 307 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 450 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE D 448 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 327 through 329 Processing sheet with id= Z, first strand: chain 'D' and resid 673 through 677 removed outlier: 6.807A pdb=" N ILE D 665 " --> pdb=" O ILE D 676 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N SER D 639 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN D 618 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE D 527 " --> pdb=" O LEU D 531 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU D 531 " --> pdb=" O ILE D 527 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 2868 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: 11.11 Time building geometry restraints manager: 11.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 8505 1.37 - 1.51: 6855 1.51 - 1.66: 9734 1.66 - 1.80: 121 1.80 - 1.95: 21 Bond restraints: 25236 Sorted by residual: bond pdb=" N ASN C 394 " pdb=" CA ASN C 394 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.85e+00 bond pdb=" N ASN D 394 " pdb=" CA ASN D 394 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.68e+00 bond pdb=" N ARG D 323 " pdb=" CA ARG D 323 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.27e-02 6.20e+03 4.73e+00 bond pdb=" N ARG C 323 " pdb=" CA ARG C 323 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.27e-02 6.20e+03 4.73e+00 bond pdb=" CG GLU C 168 " pdb=" CD GLU C 168 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.17e+00 ... (remaining 25231 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.95: 553 105.95 - 112.96: 14193 112.96 - 119.97: 8282 119.97 - 126.97: 10940 126.97 - 133.98: 286 Bond angle restraints: 34254 Sorted by residual: angle pdb=" CA ASP L 3 " pdb=" CB ASP L 3 " pdb=" CG ASP L 3 " ideal model delta sigma weight residual 112.60 108.88 3.72 1.00e+00 1.00e+00 1.38e+01 angle pdb=" CA ASP I 3 " pdb=" CB ASP I 3 " pdb=" CG ASP I 3 " ideal model delta sigma weight residual 112.60 109.05 3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" CA ASP K 3 " pdb=" CB ASP K 3 " pdb=" CG ASP K 3 " ideal model delta sigma weight residual 112.60 109.15 3.45 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CA ASP J 3 " pdb=" CB ASP J 3 " pdb=" CG ASP J 3 " ideal model delta sigma weight residual 112.60 109.23 3.37 1.00e+00 1.00e+00 1.13e+01 angle pdb=" CA ASP K 5 " pdb=" CB ASP K 5 " pdb=" CG ASP K 5 " ideal model delta sigma weight residual 112.60 109.34 3.26 1.00e+00 1.00e+00 1.06e+01 ... (remaining 34249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 13847 17.73 - 35.46: 1019 35.46 - 53.19: 212 53.19 - 70.91: 35 70.91 - 88.64: 27 Dihedral angle restraints: 15140 sinusoidal: 6022 harmonic: 9118 Sorted by residual: dihedral pdb=" CA THR C 496 " pdb=" C THR C 496 " pdb=" N ASN C 497 " pdb=" CA ASN C 497 " ideal model delta harmonic sigma weight residual 180.00 -160.60 -19.40 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA THR D 496 " pdb=" C THR D 496 " pdb=" N ASN D 497 " pdb=" CA ASN D 497 " ideal model delta harmonic sigma weight residual 180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA TYR B 660 " pdb=" C TYR B 660 " pdb=" N GLU B 661 " pdb=" CA GLU B 661 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 15137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2570 0.035 - 0.071: 917 0.071 - 0.106: 307 0.106 - 0.141: 189 0.141 - 0.177: 13 Chirality restraints: 3996 Sorted by residual: chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE C 260 " pdb=" N ILE C 260 " pdb=" C ILE C 260 " pdb=" CB ILE C 260 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA ILE B 114 " pdb=" N ILE B 114 " pdb=" C ILE B 114 " pdb=" CB ILE B 114 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 3993 not shown) Planarity restraints: 4396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 60 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 61 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 60 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO D 61 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 61 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 61 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 60 " -0.031 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO A 61 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " -0.026 5.00e-02 4.00e+02 ... (remaining 4393 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 23 2.05 - 2.76: 3892 2.76 - 3.48: 34933 3.48 - 4.19: 59751 4.19 - 4.90: 106430 Nonbonded interactions: 205029 Sorted by model distance: nonbonded pdb=" CG ASP K 5 " pdb=" N ARG K 102 " model vdw 1.339 3.350 nonbonded pdb=" CG ASP I 5 " pdb=" N ARG I 102 " model vdw 1.339 3.350 nonbonded pdb=" CG ASP J 5 " pdb=" N ARG J 102 " model vdw 1.339 3.350 nonbonded pdb=" CG ASP L 5 " pdb=" N ARG L 102 " model vdw 1.340 3.350 nonbonded pdb=" CG ASP J 3 " pdb=" N ARG J 101 " model vdw 1.341 3.350 ... (remaining 205024 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 12 5.21 5 S 88 5.16 5 C 15574 2.51 5 N 4356 2.21 5 O 4788 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: 2.360 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: 0.020 Extract box with map and model: 17.430 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.200 Process input model: 68.530 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 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 : 0.003 0.037 25236 Z= 0.181 Angle : 0.576 9.917 34254 Z= 0.308 Chirality : 0.046 0.177 3996 Planarity : 0.004 0.054 4396 Dihedral : 13.605 88.642 9328 Min Nonbonded Distance : 1.339 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3202 helix: 1.54 (0.15), residues: 1238 sheet: -0.12 (0.24), residues: 440 loop : -1.06 (0.15), residues: 1524 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 211 time to evaluate : 2.732 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 214 average time/residue: 1.2838 time to fit residues: 321.5646 Evaluate side-chains 142 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 2.798 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 3.8807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.0670 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 0.0010 chunk 96 optimal weight: 0.2980 chunk 151 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 overall best weight: 0.8728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 HIS D 247 GLN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 25236 Z= 0.186 Angle : 0.497 7.658 34254 Z= 0.261 Chirality : 0.044 0.157 3996 Planarity : 0.004 0.054 4396 Dihedral : 6.821 89.347 3568 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.44 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3202 helix: 1.54 (0.15), residues: 1230 sheet: -0.06 (0.23), residues: 500 loop : -1.03 (0.15), residues: 1472 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 169 average time/residue: 1.1958 time to fit residues: 240.4973 Evaluate side-chains 146 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 2.915 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.2505 time to fit residues: 4.8443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 289 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 232 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN D 247 GLN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 25236 Z= 0.344 Angle : 0.547 7.699 34254 Z= 0.289 Chirality : 0.047 0.154 3996 Planarity : 0.004 0.052 4396 Dihedral : 6.992 86.887 3568 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.75 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3202 helix: 1.47 (0.15), residues: 1226 sheet: -0.17 (0.24), residues: 460 loop : -0.97 (0.15), residues: 1516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 23 residues processed: 178 average time/residue: 1.1006 time to fit residues: 236.6999 Evaluate side-chains 164 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 2.937 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 7 average time/residue: 0.5292 time to fit residues: 9.1432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 290 optimal weight: 0.5980 chunk 307 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 275 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 25236 Z= 0.194 Angle : 0.488 8.089 34254 Z= 0.257 Chirality : 0.044 0.149 3996 Planarity : 0.004 0.053 4396 Dihedral : 6.806 88.499 3568 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3202 helix: 1.58 (0.15), residues: 1226 sheet: -0.09 (0.23), residues: 498 loop : -0.97 (0.15), residues: 1478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 145 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 25 residues processed: 187 average time/residue: 1.0703 time to fit residues: 241.9763 Evaluate side-chains 163 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 2.937 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.5416 time to fit residues: 7.6503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 228 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 275 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 25236 Z= 0.298 Angle : 0.525 8.610 34254 Z= 0.277 Chirality : 0.045 0.151 3996 Planarity : 0.004 0.051 4396 Dihedral : 6.855 87.805 3568 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3202 helix: 1.52 (0.15), residues: 1238 sheet: -0.13 (0.23), residues: 500 loop : -0.95 (0.15), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 145 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 32 residues processed: 191 average time/residue: 1.0726 time to fit residues: 249.2750 Evaluate side-chains 169 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 2.993 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 29 residues processed: 5 average time/residue: 0.6640 time to fit residues: 8.4681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 307 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 142 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 101 optimal weight: 0.9980 chunk 161 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 25236 Z= 0.217 Angle : 0.498 8.702 34254 Z= 0.261 Chirality : 0.045 0.149 3996 Planarity : 0.004 0.052 4396 Dihedral : 6.756 89.129 3568 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.28 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3202 helix: 1.57 (0.15), residues: 1240 sheet: -0.10 (0.23), residues: 500 loop : -0.95 (0.15), residues: 1462 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 140 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 29 residues processed: 182 average time/residue: 1.0844 time to fit residues: 240.5943 Evaluate side-chains 166 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 2.817 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 3 average time/residue: 0.2539 time to fit residues: 5.3013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 175 optimal weight: 0.0670 chunk 224 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 25236 Z= 0.299 Angle : 0.533 8.740 34254 Z= 0.279 Chirality : 0.046 0.157 3996 Planarity : 0.004 0.051 4396 Dihedral : 6.828 89.044 3568 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.06 % Favored : 95.88 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3202 helix: 1.43 (0.15), residues: 1262 sheet: -0.11 (0.23), residues: 500 loop : -0.94 (0.15), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 138 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 34 residues processed: 180 average time/residue: 1.1712 time to fit residues: 252.9398 Evaluate side-chains 167 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 3.038 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 31 residues processed: 5 average time/residue: 0.7061 time to fit residues: 8.5444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1459 > 50: distance: 55 - 95: 27.822 distance: 58 - 92: 13.100 distance: 76 - 83: 7.563 distance: 83 - 84: 6.057 distance: 84 - 85: 6.909 distance: 84 - 87: 18.312 distance: 85 - 86: 6.554 distance: 85 - 92: 9.875 distance: 87 - 88: 13.452 distance: 88 - 89: 9.023 distance: 89 - 90: 19.429 distance: 90 - 91: 23.767 distance: 92 - 93: 7.732 distance: 93 - 94: 9.994 distance: 93 - 96: 16.112 distance: 94 - 95: 26.442 distance: 94 - 100: 19.980 distance: 96 - 97: 28.768 distance: 96 - 98: 5.308 distance: 97 - 99: 22.934 distance: 100 - 101: 18.147 distance: 101 - 102: 8.852 distance: 101 - 104: 10.991 distance: 102 - 103: 29.928 distance: 102 - 109: 27.457 distance: 104 - 105: 16.675 distance: 105 - 106: 11.973 distance: 106 - 107: 9.081 distance: 106 - 108: 12.993 distance: 109 - 110: 12.423 distance: 110 - 111: 18.567 distance: 110 - 113: 20.233 distance: 111 - 112: 17.530 distance: 111 - 114: 23.917 distance: 114 - 115: 11.201 distance: 115 - 116: 12.891 distance: 115 - 118: 35.696 distance: 116 - 117: 11.432 distance: 116 - 121: 7.583 distance: 118 - 119: 29.193 distance: 118 - 120: 26.979 distance: 121 - 122: 7.392 distance: 122 - 123: 6.914 distance: 122 - 125: 4.576 distance: 123 - 124: 5.607 distance: 123 - 129: 4.213 distance: 125 - 126: 8.275 distance: 126 - 127: 12.140 distance: 126 - 128: 13.506 distance: 129 - 130: 4.009 distance: 130 - 131: 7.875 distance: 131 - 132: 22.741 distance: 131 - 135: 6.502 distance: 133 - 134: 5.882 distance: 135 - 136: 3.542 distance: 136 - 137: 9.624 distance: 136 - 139: 9.243 distance: 137 - 138: 6.814 distance: 137 - 143: 11.793 distance: 140 - 141: 8.874 distance: 140 - 142: 11.049 distance: 143 - 144: 16.173 distance: 144 - 145: 9.403 distance: 144 - 147: 14.821 distance: 145 - 146: 15.552 distance: 145 - 152: 20.898 distance: 147 - 148: 31.950 distance: 148 - 149: 11.294 distance: 149 - 150: 9.077 distance: 149 - 151: 13.391 distance: 152 - 153: 28.390 distance: 153 - 154: 18.099 distance: 153 - 156: 24.212 distance: 154 - 155: 10.361 distance: 154 - 159: 4.396 distance: 156 - 157: 26.770 distance: 156 - 158: 15.846