Starting phenix.real_space_refine (version: dev) on Fri Feb 24 02:51:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re1_24430/02_2023/7re1_24430_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re1_24430/02_2023/7re1_24430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re1_24430/02_2023/7re1_24430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re1_24430/02_2023/7re1_24430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re1_24430/02_2023/7re1_24430_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re1_24430/02_2023/7re1_24430_updated.pdb" } resolution = 2.91 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= 0.031 sd= 1.303 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 ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21825 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1415 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4557 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4557 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 558} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 789 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 62.863 45.535 117.628 1.00 65.71 S ATOM 2495 SG CYS A 306 62.249 46.786 121.192 1.00 65.13 S ATOM 2527 SG CYS A 310 63.846 43.367 120.614 1.00 59.03 S ATOM 3935 SG CYS A 487 64.664 60.713 104.014 1.00 66.11 S ATOM 5188 SG CYS A 645 63.653 62.526 107.227 1.00 71.91 S ATOM 5194 SG CYS A 646 63.003 58.807 106.758 1.00 69.76 S ATOM 10896 SG CYS E 5 112.659 64.168 54.701 1.00 81.99 S ATOM 10917 SG CYS E 8 115.804 64.423 56.437 1.00 83.65 S ATOM 11055 SG CYS E 26 114.029 67.688 55.934 1.00 81.79 S ATOM 11076 SG CYS E 29 115.354 66.267 52.940 1.00 81.74 S ATOM 11241 SG CYS E 50 93.343 81.615 51.188 1.00 86.34 S ATOM 11271 SG CYS E 55 91.833 81.488 47.640 1.00 90.55 S ATOM 11404 SG CYS E 72 94.591 84.127 48.571 1.00 83.16 S ATOM 10978 SG CYS E 16 104.655 66.442 47.289 1.00 81.05 S ATOM 10993 SG CYS E 19 105.305 62.929 45.888 1.00 83.14 S ATOM 15453 SG CYS F 5 61.276 64.849 56.971 1.00 73.73 S ATOM 15474 SG CYS F 8 64.035 65.154 54.533 1.00 77.17 S ATOM 15612 SG CYS F 26 63.417 68.190 56.551 1.00 77.53 S ATOM 15633 SG CYS F 29 60.829 67.489 54.250 1.00 78.77 S ATOM 15798 SG CYS F 50 53.526 79.656 78.077 1.00 82.02 S ATOM 15828 SG CYS F 55 49.946 80.964 78.280 1.00 88.78 S ATOM 15961 SG CYS F 72 52.280 82.603 75.866 1.00 78.64 S ATOM 15535 SG CYS F 16 52.340 67.221 62.583 1.00 72.29 S ATOM 15550 SG CYS F 19 50.379 64.076 61.484 1.00 75.11 S Time building chain proxies: 12.92, per 1000 atoms: 0.59 Number of scatterers: 21825 At special positions: 0 Unit cell: (146.59, 150.87, 181.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 151 16.00 P 77 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4437 8.00 N 3657 7.00 C 13484 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.75 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " Number of angles added : 26 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 21 sheets defined 37.8% alpha, 9.1% beta 34 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 8.03 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.545A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 169 through 199 removed outlier: 3.689A pdb=" N ALA A 176 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N CYS A 193 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.021A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.370A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 320 removed outlier: 3.828A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 449 through 458 removed outlier: 3.951A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 4.188A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 removed outlier: 3.511A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 579 removed outlier: 4.092A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.813A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 688 through 709 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 857 through 871 Proline residue: A 868 - end of helix removed outlier: 4.711A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 4.003A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 919 through 925 removed outlier: 3.939A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 32 through 78 Processing helix chain 'B' and resid 80 through 96 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.622A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.545A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.696A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 33 through 81 removed outlier: 3.508A pdb=" N GLU D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 135 through 141 removed outlier: 3.557A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 105 through 111 Processing helix chain 'E' and resid 118 through 122 Processing helix chain 'E' and resid 128 through 148 removed outlier: 3.503A pdb=" N ALA E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER E 148 " --> pdb=" O THR E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 274 Processing helix chain 'E' and resid 291 through 298 Processing helix chain 'E' and resid 312 through 324 removed outlier: 3.590A pdb=" N ALA E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 424 through 431 Processing helix chain 'E' and resid 446 through 455 removed outlier: 4.491A pdb=" N ALA E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 498 Processing helix chain 'E' and resid 516 through 525 removed outlier: 4.604A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE E 525 " --> pdb=" O VAL E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 536 No H-bonds generated for 'chain 'E' and resid 533 through 536' Processing helix chain 'E' and resid 558 through 567 removed outlier: 4.521A pdb=" N ARG E 567 " --> pdb=" O VAL E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 584 No H-bonds generated for 'chain 'E' and resid 581 through 584' Processing helix chain 'F' and resid 27 through 36 removed outlier: 3.678A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 111 removed outlier: 4.502A pdb=" N ALA F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 122 Processing helix chain 'F' and resid 128 through 147 removed outlier: 3.783A pdb=" N PHE F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 274 removed outlier: 3.794A pdb=" N VAL F 266 " --> pdb=" O SER F 263 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA F 267 " --> pdb=" O SER F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 298 removed outlier: 4.045A pdb=" N ILE F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 323 Processing helix chain 'F' and resid 381 through 390 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 431 Processing helix chain 'F' and resid 446 through 455 Processing helix chain 'F' and resid 490 through 498 Processing helix chain 'F' and resid 516 through 525 removed outlier: 3.566A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 564 Processing helix chain 'F' and resid 579 through 583 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 Processing sheet with id= B, first strand: chain 'A' and resid 31 through 33 Processing sheet with id= C, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= D, first strand: chain 'A' and resid 98 through 105 removed outlier: 4.316A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.526A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= G, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= H, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.477A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= J, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= K, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.235A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.274A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= N, first strand: chain 'E' and resid 197 through 199 Processing sheet with id= O, first strand: chain 'E' and resid 277 through 280 removed outlier: 6.616A pdb=" N TYR E 396 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU E 280 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TYR E 398 " --> pdb=" O LEU E 280 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 471 through 475 removed outlier: 6.537A pdb=" N ILE E 572 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N MET E 474 " --> pdb=" O ILE E 572 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N CYS E 574 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER E 513 " --> pdb=" O GLN E 531 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 64 through 66 Processing sheet with id= R, first strand: chain 'F' and resid 197 through 199 Processing sheet with id= S, first strand: chain 'F' and resid 277 through 280 removed outlier: 6.660A pdb=" N TYR F 396 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU F 280 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR F 398 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA F 308 " --> pdb=" O CYS F 358 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 366 through 368 removed outlier: 3.596A pdb=" N ARG F 392 " --> pdb=" O THR F 366 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 510 through 513 removed outlier: 3.863A pdb=" N THR F 547 " --> pdb=" O ILE F 512 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY F 571 " --> pdb=" O VAL F 544 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE F 546 " --> pdb=" O GLY F 571 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU F 573 " --> pdb=" O PHE F 546 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 1914 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 8.83 Time building geometry restraints manager: 10.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3343 1.28 - 1.42: 5982 1.42 - 1.55: 12521 1.55 - 1.68: 234 1.68 - 1.82: 220 Bond restraints: 22300 Sorted by residual: bond pdb=" F1 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" F1 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" F3 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" F2 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" F3 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.54e+01 ... (remaining 22295 not shown) Histogram of bond angle deviations from ideal: 98.37 - 106.13: 880 106.13 - 113.89: 12905 113.89 - 121.65: 11977 121.65 - 129.42: 4755 129.42 - 137.18: 149 Bond angle restraints: 30666 Sorted by residual: angle pdb=" N HIS E 290 " pdb=" CA HIS E 290 " pdb=" C HIS E 290 " ideal model delta sigma weight residual 113.30 104.73 8.57 1.34e+00 5.57e-01 4.09e+01 angle pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta sigma weight residual 123.00 137.18 -14.18 3.00e+00 1.11e-01 2.23e+01 angle pdb=" CA SER E 80 " pdb=" C SER E 80 " pdb=" N PHE E 81 " ideal model delta sigma weight residual 116.50 123.62 -7.12 1.63e+00 3.76e-01 1.91e+01 angle pdb=" C LYS E 288 " pdb=" N SER E 289 " pdb=" CA SER E 289 " ideal model delta sigma weight residual 122.56 115.12 7.44 1.72e+00 3.38e-01 1.87e+01 angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 129.37 -7.83 1.91e+00 2.74e-01 1.68e+01 ... (remaining 30661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 12847 34.94 - 69.89: 278 69.89 - 104.83: 18 104.83 - 139.77: 7 139.77 - 174.72: 4 Dihedral angle restraints: 13154 sinusoidal: 5597 harmonic: 7557 Sorted by residual: dihedral pdb=" CA SER E 80 " pdb=" C SER E 80 " pdb=" N PHE E 81 " pdb=" CA PHE E 81 " ideal model delta harmonic sigma weight residual 180.00 47.31 132.69 0 5.00e+00 4.00e-02 7.04e+02 dihedral pdb=" CA LYS E 189 " pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta harmonic sigma weight residual 0.00 41.52 -41.52 0 5.00e+00 4.00e-02 6.90e+01 dihedral pdb=" CA ASN F 190 " pdb=" C ASN F 190 " pdb=" N SER F 191 " pdb=" CA SER F 191 " ideal model delta harmonic sigma weight residual 180.00 138.53 41.47 0 5.00e+00 4.00e-02 6.88e+01 ... (remaining 13151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.030: 3567 1.030 - 2.059: 0 2.059 - 3.089: 0 3.089 - 4.119: 0 4.119 - 5.148: 2 Chirality restraints: 3569 Sorted by residual: chirality pdb=" C18 1N7 A1005 " pdb=" C17 1N7 A1005 " pdb=" C19 1N7 A1005 " pdb=" C6 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.53 -2.62 5.15 2.00e-01 2.50e+01 6.63e+02 chirality pdb=" C6 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C7 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.43 2.67 -5.10 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C17 1N7 A1006 " pdb=" C16 1N7 A1006 " pdb=" C18 1N7 A1006 " pdb=" O3 1N7 A1006 " both_signs ideal model delta sigma weight residual False 2.40 2.81 -0.41 2.00e-01 2.50e+01 4.16e+00 ... (remaining 3566 not shown) Planarity restraints: 3621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 52 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO E 53 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 53 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 53 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS F 444 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO F 445 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 445 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 445 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 288 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C LYS E 288 " 0.033 2.00e-02 2.50e+03 pdb=" O LYS E 288 " -0.012 2.00e-02 2.50e+03 pdb=" N SER E 289 " -0.011 2.00e-02 2.50e+03 ... (remaining 3618 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 97 2.41 - 3.03: 12895 3.03 - 3.65: 33856 3.65 - 4.28: 51939 4.28 - 4.90: 84896 Nonbonded interactions: 183683 Sorted by model distance: nonbonded pdb="MG MG A1003 " pdb=" O1A ADP A1004 " model vdw 1.787 2.170 nonbonded pdb="MG MG E 705 " pdb=" F3 AF3 E 706 " model vdw 1.881 2.120 nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1003 " model vdw 1.982 2.170 nonbonded pdb=" O2B ADP F1003 " pdb="MG MG F1004 " model vdw 1.985 2.170 nonbonded pdb="MG MG F1004 " pdb=" F3 AF3 F1005 " model vdw 2.032 2.120 ... (remaining 183678 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 'B' and (resid 7 through 22 or (resid 23 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26 through 191)) selection = (chain 'D' and (resid 7 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and (n \ ame N or name CA or name C or name O or name CB )) or resid 40 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thro \ ugh 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 590 or resid 701 through 706)) selection = chain 'F' } 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 77 5.49 5 Mg 3 5.21 5 S 151 5.16 5 C 13484 2.51 5 N 3657 2.21 5 O 4437 1.98 5 F 6 1.80 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: 2.310 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: 8.790 Check model and map are aligned: 0.320 Process input model: 68.510 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.220 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:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 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 : 0.006 0.163 22300 Z= 0.381 Angle : 0.732 14.178 30666 Z= 0.384 Chirality : 0.131 5.148 3569 Planarity : 0.004 0.052 3621 Dihedral : 14.427 174.718 8280 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 8.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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 (0.16), residues: 2541 helix: -0.47 (0.16), residues: 999 sheet: -1.00 (0.29), residues: 295 loop : -1.74 (0.17), residues: 1247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 278 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 191 outliers final: 80 residues processed: 455 average time/residue: 1.0779 time to fit residues: 577.6125 Evaluate side-chains 298 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 218 time to evaluate : 2.551 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 76 residues processed: 4 average time/residue: 0.2067 time to fit residues: 4.9559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN D 65 GLN D 105 ASN D 158 GLN E 9 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 GLN F 531 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.057 22300 Z= 0.471 Angle : 0.739 24.813 30666 Z= 0.371 Chirality : 0.046 0.263 3569 Planarity : 0.005 0.059 3621 Dihedral : 9.813 168.184 3688 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 8.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.75 (0.16), residues: 2541 helix: -0.44 (0.16), residues: 1012 sheet: -0.94 (0.29), residues: 288 loop : -1.82 (0.17), residues: 1241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 229 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 190 outliers final: 110 residues processed: 386 average time/residue: 1.0960 time to fit residues: 497.4511 Evaluate side-chains 322 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 212 time to evaluate : 2.508 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 100 residues processed: 10 average time/residue: 0.3349 time to fit residues: 8.5347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 254 optimal weight: 20.0000 chunk 209 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 108 ASN C 18 GLN D 105 ASN E 492 GLN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 22300 Z= 0.199 Angle : 0.614 23.868 30666 Z= 0.300 Chirality : 0.040 0.217 3569 Planarity : 0.004 0.047 3621 Dihedral : 9.170 153.769 3688 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 7.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.31 (0.16), residues: 2541 helix: -0.02 (0.16), residues: 1001 sheet: -0.59 (0.30), residues: 285 loop : -1.63 (0.17), residues: 1255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 217 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 104 residues processed: 353 average time/residue: 1.1045 time to fit residues: 461.4748 Evaluate side-chains 311 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 207 time to evaluate : 2.437 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 96 residues processed: 8 average time/residue: 0.6201 time to fit residues: 9.7464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 224 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN D 65 GLN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 22300 Z= 0.188 Angle : 0.601 24.090 30666 Z= 0.291 Chirality : 0.040 0.213 3569 Planarity : 0.004 0.047 3621 Dihedral : 8.741 150.814 3688 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 7.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.08 (0.16), residues: 2541 helix: 0.19 (0.17), residues: 1007 sheet: -0.48 (0.30), residues: 285 loop : -1.53 (0.17), residues: 1249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 222 time to evaluate : 2.510 Fit side-chains revert: symmetry clash outliers start: 163 outliers final: 110 residues processed: 360 average time/residue: 1.0669 time to fit residues: 453.3701 Evaluate side-chains 316 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 206 time to evaluate : 2.611 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 102 residues processed: 8 average time/residue: 0.2401 time to fit residues: 6.8626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 3.9990 chunk 142 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 186 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 213 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN D 65 GLN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 22300 Z= 0.169 Angle : 0.590 23.932 30666 Z= 0.284 Chirality : 0.040 0.202 3569 Planarity : 0.003 0.041 3621 Dihedral : 8.479 159.003 3688 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 6.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.90 (0.17), residues: 2541 helix: 0.34 (0.17), residues: 1000 sheet: -0.39 (0.30), residues: 285 loop : -1.41 (0.17), residues: 1256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 227 time to evaluate : 2.289 Fit side-chains revert: symmetry clash outliers start: 153 outliers final: 107 residues processed: 358 average time/residue: 1.0604 time to fit residues: 451.2556 Evaluate side-chains 316 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 209 time to evaluate : 2.699 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 100 residues processed: 7 average time/residue: 0.6978 time to fit residues: 10.7452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.067 22300 Z= 0.535 Angle : 0.757 25.322 30666 Z= 0.378 Chirality : 0.048 0.264 3569 Planarity : 0.005 0.050 3621 Dihedral : 8.975 172.968 3688 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer Outliers : 7.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.45 (0.16), residues: 2541 helix: -0.09 (0.16), residues: 1008 sheet: -0.93 (0.29), residues: 296 loop : -1.70 (0.17), residues: 1237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 226 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 158 outliers final: 118 residues processed: 354 average time/residue: 1.0994 time to fit residues: 458.5555 Evaluate side-chains 327 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 209 time to evaluate : 2.515 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 104 residues processed: 14 average time/residue: 0.4794 time to fit residues: 12.7093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 141 optimal weight: 0.0020 chunk 210 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 156 optimal weight: 0.0050 chunk 152 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 22300 Z= 0.163 Angle : 0.616 23.697 30666 Z= 0.298 Chirality : 0.040 0.214 3569 Planarity : 0.004 0.045 3621 Dihedral : 8.464 170.317 3688 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 6.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.02 (0.16), residues: 2541 helix: 0.25 (0.17), residues: 995 sheet: -0.43 (0.31), residues: 266 loop : -1.48 (0.17), residues: 1280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 215 time to evaluate : 2.480 Fit side-chains revert: symmetry clash outliers start: 144 outliers final: 102 residues processed: 339 average time/residue: 1.0690 time to fit residues: 430.9066 Evaluate side-chains 314 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 212 time to evaluate : 2.464 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 98 residues processed: 4 average time/residue: 0.4923 time to fit residues: 5.9876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 GLN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 22300 Z= 0.326 Angle : 0.661 24.716 30666 Z= 0.323 Chirality : 0.043 0.236 3569 Planarity : 0.004 0.044 3621 Dihedral : 8.549 178.122 3688 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 6.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.14 (0.16), residues: 2541 helix: 0.18 (0.16), residues: 989 sheet: -0.74 (0.29), residues: 298 loop : -1.52 (0.17), residues: 1254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 216 time to evaluate : 2.520 Fit side-chains revert: symmetry clash outliers start: 133 outliers final: 110 residues processed: 329 average time/residue: 1.0828 time to fit residues: 421.9358 Evaluate side-chains 314 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 204 time to evaluate : 2.594 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 103 residues processed: 7 average time/residue: 0.3018 time to fit residues: 6.6775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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-4877/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-4877/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-4877/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-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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: 59.3407 > 50: distance: 38 - 59: 17.734 distance: 42 - 67: 21.731 distance: 55 - 59: 15.092 distance: 59 - 60: 16.552 distance: 60 - 61: 5.327 distance: 60 - 63: 6.585 distance: 61 - 62: 12.426 distance: 61 - 67: 18.641 distance: 63 - 64: 21.510 distance: 64 - 65: 35.020 distance: 64 - 66: 32.628 distance: 67 - 68: 23.876 distance: 68 - 69: 37.584 distance: 68 - 71: 14.985 distance: 69 - 70: 8.497 distance: 69 - 78: 51.248 distance: 71 - 72: 7.367 distance: 72 - 73: 10.779 distance: 73 - 74: 5.194 distance: 74 - 75: 16.025 distance: 75 - 76: 19.594 distance: 75 - 77: 12.509 distance: 78 - 79: 8.235 distance: 79 - 80: 4.798 distance: 79 - 82: 8.636 distance: 80 - 81: 40.220 distance: 80 - 87: 18.450 distance: 82 - 83: 10.003 distance: 83 - 84: 13.249 distance: 84 - 85: 24.730 distance: 85 - 86: 26.879 distance: 87 - 88: 6.963 distance: 88 - 89: 14.664 distance: 88 - 91: 12.861 distance: 89 - 90: 25.686 distance: 89 - 95: 6.200 distance: 91 - 92: 22.428 distance: 92 - 93: 20.253 distance: 92 - 94: 5.444 distance: 96 - 97: 5.871 distance: 96 - 99: 9.751 distance: 97 - 98: 16.446 distance: 97 - 103: 16.909 distance: 99 - 100: 8.702 distance: 100 - 101: 11.340 distance: 103 - 104: 23.993 distance: 104 - 105: 13.360 distance: 104 - 107: 23.039 distance: 105 - 106: 18.433 distance: 105 - 111: 16.251 distance: 106 - 132: 45.019 distance: 107 - 108: 6.856 distance: 108 - 109: 20.833 distance: 108 - 110: 24.666 distance: 111 - 112: 8.324 distance: 112 - 113: 12.824 distance: 112 - 115: 16.310 distance: 113 - 114: 10.150 distance: 113 - 119: 7.687 distance: 114 - 140: 10.689 distance: 115 - 116: 7.539 distance: 116 - 117: 12.098 distance: 116 - 118: 5.520 distance: 119 - 120: 4.135 distance: 120 - 121: 15.345 distance: 120 - 123: 10.725 distance: 121 - 122: 8.143 distance: 121 - 124: 9.792 distance: 122 - 148: 17.273 distance: 124 - 125: 13.110 distance: 125 - 126: 22.389 distance: 125 - 128: 8.495 distance: 126 - 127: 18.732 distance: 126 - 132: 6.597 distance: 127 - 156: 22.107 distance: 128 - 129: 15.094 distance: 129 - 130: 23.050 distance: 129 - 131: 30.164 distance: 132 - 133: 9.764 distance: 133 - 134: 20.458 distance: 133 - 136: 13.452 distance: 134 - 135: 9.002 distance: 134 - 140: 5.109 distance: 135 - 164: 16.470 distance: 136 - 137: 10.654 distance: 137 - 138: 7.383 distance: 137 - 139: 13.041