Starting phenix.real_space_refine (version: dev) on Sun Feb 26 15:38:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtc_32778/02_2023/7wtc_32778_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtc_32778/02_2023/7wtc_32778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtc_32778/02_2023/7wtc_32778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtc_32778/02_2023/7wtc_32778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtc_32778/02_2023/7wtc_32778_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtc_32778/02_2023/7wtc_32778_updated.pdb" } resolution = 4.0 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 Process input model Symmetric amino acids flipped Residue "A GLU 449": "OE1" <-> "OE2" Residue "A GLU 1001": "OE1" <-> "OE2" Residue "A PHE 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B GLU 936": "OE1" <-> "OE2" Residue "B GLU 1146": "OE1" <-> "OE2" Residue "C GLU 691": "OE1" <-> "OE2" Residue "C TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 932": "OE1" <-> "OE2" Residue "C GLU 1079": "OE1" <-> "OE2" Residue "D GLU 946": "OE1" <-> "OE2" Residue "D GLU 1047": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 28418 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8869 Classifications: {'peptide': 1146} Link IDs: {'CIS': 1, 'PTRANS': 65, 'TRANS': 1079} Chain: "B" Number of atoms: 8877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8877 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 65, 'TRANS': 1081} Chain: "C" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "D" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'ACO': 1, 'BTI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'ACO': 1, 'BTI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.35, per 1000 atoms: 0.54 Number of scatterers: 28418 At special positions: 0 Unit cell: (161.7, 162.8, 136.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 172 16.00 P 6 15.00 O 5301 8.00 N 4945 7.00 C 17994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 786 " distance=2.03 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.02 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 786 " distance=2.02 Simple disulfide: pdb=" SG CYS D 752 " - pdb=" SG CYS D 786 " distance=2.02 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.45 Conformation dependent library (CDL) restraints added in 4.3 seconds 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6738 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 146 helices and 31 sheets defined 38.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 76 through 79 No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 92 through 97 removed outlier: 4.186A pdb=" N TYR A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 97' Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.602A pdb=" N TYR A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 4.095A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 302 Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.676A pdb=" N THR A 334 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 357 through 360 No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 469 through 472 No H-bonds generated for 'chain 'A' and resid 469 through 472' Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 573 through 576 No H-bonds generated for 'chain 'A' and resid 573 through 576' Processing helix chain 'A' and resid 584 through 597 removed outlier: 3.674A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 623 through 633 removed outlier: 3.574A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 669 Processing helix chain 'A' and resid 683 through 696 Processing helix chain 'A' and resid 720 through 733 Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 810 through 816 Processing helix chain 'A' and resid 828 through 842 Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 861 through 864 No H-bonds generated for 'chain 'A' and resid 861 through 864' Processing helix chain 'A' and resid 871 through 881 Processing helix chain 'A' and resid 886 through 900 removed outlier: 3.887A pdb=" N LYS A 891 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL A 895 " --> pdb=" O LYS A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 924 Processing helix chain 'A' and resid 928 through 933 Processing helix chain 'A' and resid 942 through 949 Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 978 through 981 No H-bonds generated for 'chain 'A' and resid 978 through 981' Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1004 through 1012 Processing helix chain 'A' and resid 1014 through 1027 Processing helix chain 'A' and resid 1035 through 1039 Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 76 through 79 No H-bonds generated for 'chain 'B' and resid 76 through 79' Processing helix chain 'B' and resid 92 through 97 removed outlier: 4.232A pdb=" N TYR B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 97' Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 210 through 227 Processing helix chain 'B' and resid 285 through 302 Processing helix chain 'B' and resid 331 through 340 removed outlier: 3.868A pdb=" N THR B 334 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR B 340 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'B' and resid 357 through 360 No H-bonds generated for 'chain 'B' and resid 357 through 360' Processing helix chain 'B' and resid 436 through 449 Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 485 through 487 No H-bonds generated for 'chain 'B' and resid 485 through 487' Processing helix chain 'B' and resid 496 through 509 Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 550 through 559 Processing helix chain 'B' and resid 572 through 577 Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.799A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 596 Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 631 removed outlier: 3.611A pdb=" N LEU B 630 " --> pdb=" O ARG B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 Processing helix chain 'B' and resid 683 through 696 Processing helix chain 'B' and resid 720 through 733 Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 799 through 801 No H-bonds generated for 'chain 'B' and resid 799 through 801' Processing helix chain 'B' and resid 810 through 816 Processing helix chain 'B' and resid 828 through 843 removed outlier: 3.573A pdb=" N TRP B 838 " --> pdb=" O TYR B 834 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 854 Processing helix chain 'B' and resid 861 through 864 No H-bonds generated for 'chain 'B' and resid 861 through 864' Processing helix chain 'B' and resid 871 through 881 Processing helix chain 'B' and resid 887 through 901 removed outlier: 4.264A pdb=" N VAL B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 924 Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 942 through 949 Processing helix chain 'B' and resid 961 through 968 Processing helix chain 'B' and resid 978 through 981 No H-bonds generated for 'chain 'B' and resid 978 through 981' Processing helix chain 'B' and resid 988 through 998 Processing helix chain 'B' and resid 1004 through 1012 Processing helix chain 'B' and resid 1014 through 1027 Processing helix chain 'B' and resid 1035 through 1039 Processing helix chain 'C' and resid 496 through 509 Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 550 through 559 Processing helix chain 'C' and resid 572 through 577 Processing helix chain 'C' and resid 587 through 589 No H-bonds generated for 'chain 'C' and resid 587 through 589' Processing helix chain 'C' and resid 591 through 597 Processing helix chain 'C' and resid 609 through 617 Processing helix chain 'C' and resid 623 through 631 removed outlier: 3.668A pdb=" N LEU C 630 " --> pdb=" O ARG C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 669 Processing helix chain 'C' and resid 683 through 696 Processing helix chain 'C' and resid 720 through 733 Processing helix chain 'C' and resid 749 through 762 removed outlier: 4.305A pdb=" N ARG C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 789 Processing helix chain 'C' and resid 799 through 801 No H-bonds generated for 'chain 'C' and resid 799 through 801' Processing helix chain 'C' and resid 810 through 816 Processing helix chain 'C' and resid 829 through 845 removed outlier: 3.956A pdb=" N GLY C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU C 844 " --> pdb=" O GLY C 840 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR C 845 " --> pdb=" O ALA C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 852 No H-bonds generated for 'chain 'C' and resid 850 through 852' Processing helix chain 'C' and resid 861 through 864 No H-bonds generated for 'chain 'C' and resid 861 through 864' Processing helix chain 'C' and resid 871 through 881 Processing helix chain 'C' and resid 887 through 901 removed outlier: 4.162A pdb=" N VAL C 895 " --> pdb=" O LYS C 891 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU C 896 " --> pdb=" O LYS C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 923 Processing helix chain 'C' and resid 928 through 933 Processing helix chain 'C' and resid 942 through 949 Processing helix chain 'C' and resid 961 through 968 Processing helix chain 'C' and resid 978 through 981 No H-bonds generated for 'chain 'C' and resid 978 through 981' Processing helix chain 'C' and resid 988 through 997 removed outlier: 3.549A pdb=" N LYS C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1012 Processing helix chain 'C' and resid 1014 through 1027 removed outlier: 3.593A pdb=" N THR C1026 " --> pdb=" O ASP C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1040 Processing helix chain 'D' and resid 496 through 510 Processing helix chain 'D' and resid 542 through 547 Processing helix chain 'D' and resid 550 through 559 Processing helix chain 'D' and resid 572 through 577 Processing helix chain 'D' and resid 584 through 597 Proline residue: D 592 - end of helix Processing helix chain 'D' and resid 609 through 617 Processing helix chain 'D' and resid 623 through 633 Processing helix chain 'D' and resid 656 through 668 Processing helix chain 'D' and resid 683 through 696 Processing helix chain 'D' and resid 720 through 732 Processing helix chain 'D' and resid 749 through 762 removed outlier: 4.406A pdb=" N ARG D 762 " --> pdb=" O SER D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 789 Processing helix chain 'D' and resid 811 through 817 Processing helix chain 'D' and resid 828 through 845 removed outlier: 4.191A pdb=" N GLY D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR D 845 " --> pdb=" O ALA D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 854 removed outlier: 4.257A pdb=" N MET D 854 " --> pdb=" O THR D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 864 Processing helix chain 'D' and resid 868 through 880 removed outlier: 4.645A pdb=" N THR D 872 " --> pdb=" O GLY D 868 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN D 873 " --> pdb=" O GLY D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 901 removed outlier: 3.737A pdb=" N LYS D 891 " --> pdb=" O PHE D 887 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS D 892 " --> pdb=" O LYS D 888 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 893 " --> pdb=" O GLU D 889 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 895 " --> pdb=" O LYS D 891 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN D 898 " --> pdb=" O TYR D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 924 Processing helix chain 'D' and resid 928 through 933 Processing helix chain 'D' and resid 942 through 949 Processing helix chain 'D' and resid 961 through 967 Processing helix chain 'D' and resid 978 through 981 No H-bonds generated for 'chain 'D' and resid 978 through 981' Processing helix chain 'D' and resid 989 through 997 Processing helix chain 'D' and resid 1004 through 1012 Processing helix chain 'D' and resid 1014 through 1027 Processing helix chain 'D' and resid 1035 through 1039 Processing sheet with id= A, first strand: chain 'A' and resid 137 through 139 removed outlier: 6.686A pdb=" N ARG A 62 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N VAL A 42 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL A 64 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLU A 82 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N TYR A 67 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR A 84 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 191 through 195 removed outlier: 3.538A pdb=" N ILE A 192 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 262 through 264 removed outlier: 3.913A pdb=" N ILE A 245 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU A 313 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE A 322 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 249 through 251 Processing sheet with id= E, first strand: chain 'A' and resid 275 through 277 removed outlier: 4.213A pdb=" N VAL A 427 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 396 through 398 Processing sheet with id= G, first strand: chain 'A' and resid 564 through 567 Processing sheet with id= H, first strand: chain 'A' and resid 767 through 772 removed outlier: 3.898A pdb=" N ILE A 737 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET A 604 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU A 642 " --> pdb=" O MET A 604 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ASN A 606 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1047 through 1051 removed outlier: 6.841A pdb=" N PHE A1077 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL A1065 " --> pdb=" O GLN A1075 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN A1075 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1119 through 1123 removed outlier: 6.918A pdb=" N VAL A1139 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE A1123 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU A1137 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A1149 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A1139 " --> pdb=" O THR A1147 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR A1147 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 62 through 64 removed outlier: 3.700A pdb=" N VAL B 64 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 42 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA B 113 " --> pdb=" O MET B 41 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG B 137 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 65 through 67 Processing sheet with id= M, first strand: chain 'B' and resid 204 through 207 Processing sheet with id= N, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.689A pdb=" N GLU B 324 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU B 313 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N PHE B 322 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 249 through 251 Processing sheet with id= P, first strand: chain 'B' and resid 275 through 277 removed outlier: 4.167A pdb=" N VAL B 427 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 564 through 566 Processing sheet with id= R, first strand: chain 'B' and resid 767 through 771 removed outlier: 7.337A pdb=" N LEU B 642 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 1046 through 1051 removed outlier: 3.912A pdb=" N GLU B1046 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N PHE B1077 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL B1065 " --> pdb=" O GLN B1075 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN B1075 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1146 through 1148 removed outlier: 3.526A pdb=" N THR B1147 " --> pdb=" O LEU B1140 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP B1122 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER B1141 " --> pdb=" O VAL B1120 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL B1120 " --> pdb=" O SER B1141 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 564 through 567 Processing sheet with id= V, first strand: chain 'C' and resid 603 through 605 removed outlier: 6.856A pdb=" N VAL C 673 " --> pdb=" O MET C 641 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 699 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL C 676 " --> pdb=" O VAL C 699 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU C 701 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE C 737 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE C 704 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N CYS C 739 " --> pdb=" O ILE C 704 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 1047 through 1049 removed outlier: 6.612A pdb=" N PHE C1077 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL C1065 " --> pdb=" O GLN C1075 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN C1075 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 1135 through 1141 removed outlier: 3.589A pdb=" N GLN C1135 " --> pdb=" O SER C1151 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL C1149 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL C1139 " --> pdb=" O THR C1147 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C1147 " --> pdb=" O VAL C1139 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 1157 through 1160 removed outlier: 6.720A pdb=" N GLU C1176 " --> pdb=" O ARG C1158 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 564 through 566 Processing sheet with id= AA, first strand: chain 'D' and resid 768 through 772 removed outlier: 6.561A pdb=" N LEU D 738 " --> pdb=" O HIS D 769 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N HIS D 771 " --> pdb=" O LEU D 738 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE D 740 " --> pdb=" O HIS D 771 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASN D 606 " --> pdb=" O LEU D 642 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 1047 through 1050 removed outlier: 6.676A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 1129 through 1131 removed outlier: 3.717A pdb=" N ALA D1129 " --> pdb=" O VAL D1157 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 1111 through 1113 removed outlier: 4.089A pdb=" N LEU D1175 " --> pdb=" O ILE D1112 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 1119 through 1123 removed outlier: 7.043A pdb=" N VAL D1139 " --> pdb=" O ILE D1121 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE D1123 " --> pdb=" O LEU D1137 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU D1137 " --> pdb=" O ILE D1123 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL D1149 " --> pdb=" O LEU D1137 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL D1139 " --> pdb=" O THR D1147 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR D1147 " --> pdb=" O VAL D1139 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2859 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: 11.72 Time building geometry restraints manager: 13.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4816 1.31 - 1.43: 7257 1.43 - 1.56: 16642 1.56 - 1.69: 31 1.69 - 1.82: 298 Bond restraints: 29044 Sorted by residual: bond pdb=" C6 BTI C1900 " pdb=" S1 BTI C1900 " ideal model delta sigma weight residual 1.811 1.441 0.370 2.00e-02 2.50e+03 3.43e+02 bond pdb=" C6 BTI B2002 " pdb=" S1 BTI B2002 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C6 BTI A1201 " pdb=" S1 BTI A1201 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.38e+02 bond pdb=" C6 BTI D1900 " pdb=" S1 BTI D1900 " ideal model delta sigma weight residual 1.811 1.444 0.367 2.00e-02 2.50e+03 3.37e+02 bond pdb=" C3 BTI A1201 " pdb=" N3 BTI A1201 " ideal model delta sigma weight residual 1.356 1.577 -0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 29039 not shown) Histogram of bond angle deviations from ideal: 86.62 - 96.65: 2 96.65 - 106.69: 1157 106.69 - 116.72: 19254 116.72 - 126.75: 18596 126.75 - 136.79: 366 Bond angle restraints: 39375 Sorted by residual: angle pdb=" N PRO C 536 " pdb=" CD PRO C 536 " pdb=" CG PRO C 536 " ideal model delta sigma weight residual 103.20 86.62 16.58 1.50e+00 4.44e-01 1.22e+02 angle pdb=" CA PRO C 536 " pdb=" N PRO C 536 " pdb=" CD PRO C 536 " ideal model delta sigma weight residual 112.00 102.32 9.68 1.40e+00 5.10e-01 4.78e+01 angle pdb=" CA PRO C 536 " pdb=" CB PRO C 536 " pdb=" CG PRO C 536 " ideal model delta sigma weight residual 104.50 92.39 12.11 1.90e+00 2.77e-01 4.07e+01 angle pdb=" C LEU B 260 " pdb=" N TYR B 261 " pdb=" CA TYR B 261 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.42e+01 angle pdb=" N VAL D1065 " pdb=" CA VAL D1065 " pdb=" C VAL D1065 " ideal model delta sigma weight residual 112.90 107.47 5.43 9.60e-01 1.09e+00 3.21e+01 ... (remaining 39370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 15890 17.79 - 35.58: 1401 35.58 - 53.37: 187 53.37 - 71.16: 43 71.16 - 88.95: 28 Dihedral angle restraints: 17549 sinusoidal: 7052 harmonic: 10497 Sorted by residual: dihedral pdb=" CB CYS B 752 " pdb=" SG CYS B 752 " pdb=" SG CYS B 786 " pdb=" CB CYS B 786 " ideal model delta sinusoidal sigma weight residual -86.00 -174.83 88.83 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS C 752 " pdb=" SG CYS C 752 " pdb=" SG CYS C 786 " pdb=" CB CYS C 786 " ideal model delta sinusoidal sigma weight residual 93.00 177.92 -84.92 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS D 752 " pdb=" SG CYS D 752 " pdb=" SG CYS D 786 " pdb=" CB CYS D 786 " ideal model delta sinusoidal sigma weight residual 93.00 173.77 -80.77 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 17546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3472 0.055 - 0.110: 780 0.110 - 0.165: 107 0.165 - 0.220: 14 0.220 - 0.275: 5 Chirality restraints: 4378 Sorted by residual: chirality pdb=" CB THR B 908 " pdb=" CA THR B 908 " pdb=" OG1 THR B 908 " pdb=" CG2 THR B 908 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BTI B2002 " pdb=" C4 BTI B2002 " pdb=" C6 BTI B2002 " pdb=" N3 BTI B2002 " both_signs ideal model delta sigma weight residual False 2.73 2.99 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA THR B 908 " pdb=" N THR B 908 " pdb=" C THR B 908 " pdb=" CB THR B 908 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4375 not shown) Planarity restraints: 5171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 535 " -0.059 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO C 536 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 536 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 536 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 542 " -0.185 9.50e-02 1.11e+02 8.33e-02 4.93e+00 pdb=" NE ARG A 542 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 542 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 542 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 542 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 947 " -0.014 2.00e-02 2.50e+03 1.63e-02 4.66e+00 pdb=" CG PHE A 947 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 947 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 947 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 947 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE A 947 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 947 " -0.015 2.00e-02 2.50e+03 ... (remaining 5168 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 569 2.63 - 3.20: 27577 3.20 - 3.76: 46981 3.76 - 4.33: 61851 4.33 - 4.90: 97557 Nonbonded interactions: 234535 Sorted by model distance: nonbonded pdb=" NH1 ARG A 542 " pdb=" O ILE A 634 " model vdw 2.060 2.520 nonbonded pdb=" OD2 ASP B 586 " pdb=" OH TYR B 845 " model vdw 2.070 2.440 nonbonded pdb=" OD2 ASP B 343 " pdb=" ND1 HIS B 346 " model vdw 2.102 2.520 nonbonded pdb=" O ALA C1132 " pdb=" OG SER C1151 " model vdw 2.109 2.440 nonbonded pdb=" O SER D 523 " pdb=" NH1 ARG D1036 " model vdw 2.117 2.520 ... (remaining 234530 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' and resid 33 through 1178) selection = (chain 'B' and resid 33 through 1178) } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 172 5.16 5 C 17994 2.51 5 N 4945 2.21 5 O 5301 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 7.510 Check model and map are aligned: 0.410 Process input model: 74.940 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.260 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 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 : 0.008 0.370 29044 Z= 0.520 Angle : 0.823 16.581 39375 Z= 0.441 Chirality : 0.048 0.275 4378 Planarity : 0.006 0.083 5171 Dihedral : 13.694 88.949 10799 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.97 % Favored : 91.95 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.78 (0.14), residues: 3653 helix: 0.61 (0.14), residues: 1415 sheet: -0.08 (0.23), residues: 511 loop : -1.63 (0.14), residues: 1727 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 276 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 278 average time/residue: 0.4477 time to fit residues: 196.4098 Evaluate side-chains 216 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 3.495 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6417 time to fit residues: 5.6500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 7.9990 chunk 275 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 chunk 94 optimal weight: 0.0970 chunk 186 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 436 HIS A 479 GLN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1040 GLN ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 29044 Z= 0.274 Angle : 0.692 10.163 39375 Z= 0.354 Chirality : 0.045 0.262 4378 Planarity : 0.005 0.064 5171 Dihedral : 5.615 58.891 3999 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.45 % Favored : 92.44 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.88 (0.14), residues: 3653 helix: 0.50 (0.13), residues: 1430 sheet: -0.17 (0.23), residues: 497 loop : -1.67 (0.14), residues: 1726 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 238 average time/residue: 0.4324 time to fit residues: 166.7986 Evaluate side-chains 221 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 206 time to evaluate : 3.405 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2731 time to fit residues: 12.4695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 275 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 331 optimal weight: 8.9990 chunk 357 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 328 optimal weight: 10.0000 chunk 112 optimal weight: 0.2980 chunk 265 optimal weight: 5.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 208 HIS ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 29044 Z= 0.241 Angle : 0.655 10.744 39375 Z= 0.334 Chirality : 0.044 0.211 4378 Planarity : 0.005 0.044 5171 Dihedral : 5.525 56.346 3999 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.69 % Favored : 92.28 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.90 (0.14), residues: 3653 helix: 0.52 (0.13), residues: 1435 sheet: -0.24 (0.24), residues: 483 loop : -1.69 (0.14), residues: 1735 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 225 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 21 residues processed: 260 average time/residue: 0.4257 time to fit residues: 181.5640 Evaluate side-chains 226 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 3.213 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2856 time to fit residues: 15.8451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 6.9990 chunk 248 optimal weight: 30.0000 chunk 171 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 222 optimal weight: 20.0000 chunk 332 optimal weight: 0.0060 chunk 351 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 314 optimal weight: 20.0000 chunk 94 optimal weight: 0.8980 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS A 898 ASN A 899 GLN ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 ASN ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1093 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 29044 Z= 0.178 Angle : 0.616 10.701 39375 Z= 0.306 Chirality : 0.043 0.213 4378 Planarity : 0.004 0.040 5171 Dihedral : 5.325 59.430 3999 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.25 % Favored : 92.72 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.71 (0.14), residues: 3653 helix: 0.71 (0.14), residues: 1438 sheet: -0.09 (0.24), residues: 481 loop : -1.64 (0.14), residues: 1734 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 4.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 25 residues processed: 247 average time/residue: 0.4440 time to fit residues: 179.9729 Evaluate side-chains 230 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 205 time to evaluate : 3.215 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2755 time to fit residues: 16.9712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 261 optimal weight: 0.0170 chunk 145 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 315 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 overall best weight: 1.3420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 414 GLN A 432 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 653 ASN ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 421 HIS ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 29044 Z= 0.169 Angle : 0.599 9.872 39375 Z= 0.296 Chirality : 0.042 0.224 4378 Planarity : 0.004 0.039 5171 Dihedral : 5.195 59.935 3999 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.31 % Favored : 92.66 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.56 (0.14), residues: 3653 helix: 0.86 (0.14), residues: 1432 sheet: -0.02 (0.23), residues: 495 loop : -1.57 (0.15), residues: 1726 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 222 time to evaluate : 3.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 12 residues processed: 256 average time/residue: 0.4331 time to fit residues: 180.1348 Evaluate side-chains 220 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 208 time to evaluate : 3.609 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3288 time to fit residues: 11.8047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 0.4980 chunk 316 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 206 optimal weight: 0.3980 chunk 86 optimal weight: 0.1980 chunk 352 optimal weight: 10.0000 chunk 292 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 923 GLN ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 29044 Z= 0.180 Angle : 0.615 10.523 39375 Z= 0.304 Chirality : 0.043 0.217 4378 Planarity : 0.004 0.039 5171 Dihedral : 5.183 59.168 3999 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.45 % Favored : 92.50 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.54 (0.14), residues: 3653 helix: 0.89 (0.14), residues: 1433 sheet: -0.06 (0.23), residues: 493 loop : -1.56 (0.15), residues: 1727 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 217 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 236 average time/residue: 0.4541 time to fit residues: 172.2956 Evaluate side-chains 222 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 3.405 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3202 time to fit residues: 13.5611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 chunk 257 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 350 optimal weight: 8.9990 chunk 219 optimal weight: 1.9990 chunk 213 optimal weight: 0.1980 chunk 161 optimal weight: 3.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 ASN ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1161 HIS ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 29044 Z= 0.210 Angle : 0.640 10.398 39375 Z= 0.316 Chirality : 0.043 0.207 4378 Planarity : 0.004 0.040 5171 Dihedral : 5.236 59.630 3999 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.58 % Favored : 92.36 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3653 helix: 0.84 (0.14), residues: 1432 sheet: -0.25 (0.23), residues: 505 loop : -1.58 (0.15), residues: 1716 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 219 time to evaluate : 3.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 239 average time/residue: 0.4555 time to fit residues: 172.7191 Evaluate side-chains 219 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 3.433 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3242 time to fit residues: 10.6901 ------------------------------------------------------------------------------- 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-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: 50.4324 > 50: distance: 30 - 33: 13.580 distance: 33 - 34: 19.001 distance: 34 - 35: 13.849 distance: 34 - 37: 21.864 distance: 35 - 36: 4.900 distance: 35 - 39: 9.581 distance: 37 - 38: 35.462 distance: 39 - 40: 5.814 distance: 40 - 41: 28.872 distance: 40 - 43: 5.253 distance: 41 - 42: 24.127 distance: 41 - 47: 24.717 distance: 43 - 44: 15.226 distance: 44 - 45: 7.672 distance: 44 - 46: 6.528 distance: 47 - 48: 14.901 distance: 47 - 53: 18.279 distance: 48 - 49: 45.368 distance: 48 - 51: 35.251 distance: 49 - 50: 28.031 distance: 49 - 54: 41.237 distance: 51 - 52: 16.463 distance: 52 - 53: 19.334 distance: 54 - 55: 7.682 distance: 54 - 60: 26.994 distance: 55 - 56: 29.450 distance: 55 - 58: 14.778 distance: 56 - 57: 21.302 distance: 56 - 61: 21.616 distance: 58 - 59: 40.879 distance: 59 - 60: 21.839 distance: 61 - 62: 20.400 distance: 62 - 63: 23.379 distance: 62 - 65: 17.222 distance: 63 - 64: 26.047 distance: 63 - 69: 45.009 distance: 65 - 66: 10.504 distance: 66 - 67: 41.663 distance: 66 - 68: 39.264 distance: 69 - 70: 11.386 distance: 70 - 71: 9.703 distance: 70 - 73: 20.295 distance: 71 - 72: 8.979 distance: 71 - 77: 9.701 distance: 73 - 74: 3.140 distance: 74 - 75: 15.336 distance: 74 - 76: 17.964 distance: 77 - 78: 6.658 distance: 78 - 79: 11.393 distance: 78 - 81: 14.759 distance: 79 - 80: 14.076 distance: 79 - 85: 3.223 distance: 81 - 82: 5.999 distance: 82 - 83: 9.108 distance: 82 - 84: 6.549 distance: 85 - 86: 9.258 distance: 86 - 87: 13.421 distance: 86 - 89: 15.789 distance: 87 - 88: 7.596 distance: 87 - 94: 7.714 distance: 88 - 116: 11.906 distance: 89 - 90: 21.967 distance: 90 - 91: 8.220 distance: 91 - 92: 17.233 distance: 91 - 93: 13.938 distance: 94 - 95: 8.648 distance: 95 - 96: 10.491 distance: 95 - 98: 7.085 distance: 96 - 97: 8.232 distance: 96 - 99: 14.009 distance: 97 - 125: 14.774 distance: 100 - 101: 3.698 distance: 100 - 103: 10.077 distance: 101 - 102: 7.817 distance: 101 - 107: 4.770 distance: 102 - 133: 11.146 distance: 103 - 104: 5.939 distance: 104 - 105: 5.594