Starting phenix.real_space_refine on Mon May 19 14:29:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qec_18351/05_2025/8qec_18351_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qec_18351/05_2025/8qec_18351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qec_18351/05_2025/8qec_18351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qec_18351/05_2025/8qec_18351.map" model { file = "/net/cci-nas-00/data/ceres_data/8qec_18351/05_2025/8qec_18351_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qec_18351/05_2025/8qec_18351_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.004 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5951 2.51 5 N 1405 2.21 5 O 1690 1.98 5 H 8699 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17802 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 17510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 17510 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 47, 'TRANS': 1053} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'ERG': 1, 'Q7G': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 9.07, per 1000 atoms: 0.51 Number of scatterers: 17802 At special positions: 0 Unit cell: (88.976, 102.912, 162.944, 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 57 16.00 O 1690 8.00 N 1405 7.00 C 5951 6.00 H 8699 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 41 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 480 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 868 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 869 " - pdb=" SG CYS A 891 " distance=2.03 Simple disulfide: pdb=" SG CYS A 879 " - pdb=" SG CYS A 888 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 1 " - " ASN A 900 " " NAG C 1 " - " ASN A 940 " " NAG D 1 " - " ASN A 401 " " NAG E 1 " - " ASN A 513 " Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 59.8% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 65 through 71 removed outlier: 4.351A pdb=" N GLU A 70 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.878A pdb=" N LYS A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.523A pdb=" N PHE A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 145 through 158 removed outlier: 3.547A pdb=" N CYS A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.613A pdb=" N LEU A 183 " --> pdb=" O TYR A 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 279 Processing helix chain 'A' and resid 309 through 337 Processing helix chain 'A' and resid 337 through 359 removed outlier: 3.652A pdb=" N ILE A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 389 Processing helix chain 'A' and resid 408 through 420 removed outlier: 3.831A pdb=" N ASP A 417 " --> pdb=" O HIS A 413 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 418 " --> pdb=" O TRP A 414 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.554A pdb=" N LEU A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 477 through 480 Processing helix chain 'A' and resid 515 through 531 removed outlier: 3.801A pdb=" N ASN A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 553 Processing helix chain 'A' and resid 557 through 576 removed outlier: 3.639A pdb=" N VAL A 561 " --> pdb=" O ASP A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 606 removed outlier: 3.565A pdb=" N GLY A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 Processing helix chain 'A' and resid 614 through 619 removed outlier: 3.535A pdb=" N GLU A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 630 through 646 removed outlier: 3.810A pdb=" N PHE A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 635 " --> pdb=" O ASP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 682 removed outlier: 4.019A pdb=" N ARG A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Proline residue: A 665 - end of helix removed outlier: 3.818A pdb=" N CYS A 677 " --> pdb=" O CYS A 673 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE A 678 " --> pdb=" O GLN A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.601A pdb=" N PHE A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 removed outlier: 3.765A pdb=" N SER A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 747 removed outlier: 3.691A pdb=" N THR A 747 " --> pdb=" O PHE A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 763 Processing helix chain 'A' and resid 766 through 770 Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.967A pdb=" N ALA A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 775 through 780' Processing helix chain 'A' and resid 785 through 794 removed outlier: 3.644A pdb=" N TYR A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 832 through 840 Processing helix chain 'A' and resid 852 through 861 removed outlier: 3.552A pdb=" N ASP A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 861 " --> pdb=" O TYR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 897 removed outlier: 4.028A pdb=" N TRP A 897 " --> pdb=" O GLN A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 918 removed outlier: 4.139A pdb=" N MET A 911 " --> pdb=" O GLY A 907 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 915 " --> pdb=" O MET A 911 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 916 " --> pdb=" O GLU A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.516A pdb=" N ILE A 963 " --> pdb=" O GLN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 removed outlier: 3.844A pdb=" N VAL A 992 " --> pdb=" O ILE A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 995 No H-bonds generated for 'chain 'A' and resid 993 through 995' Processing helix chain 'A' and resid 996 through 1021 removed outlier: 3.534A pdb=" N THR A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1048 Processing helix chain 'A' and resid 1053 through 1079 removed outlier: 3.794A pdb=" N VAL A1057 " --> pdb=" O ALA A1053 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY A1064 " --> pdb=" O ILE A1060 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS A1070 " --> pdb=" O GLY A1066 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A1073 " --> pdb=" O PHE A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1106 removed outlier: 5.635A pdb=" N GLU A1101 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER A1102 " --> pdb=" O THR A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1119 removed outlier: 3.907A pdb=" N LYS A1111 " --> pdb=" O ILE A1107 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A1112 " --> pdb=" O THR A1108 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A1117 " --> pdb=" O ILE A1113 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A1118 " --> pdb=" O GLY A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1129 removed outlier: 3.949A pdb=" N ASP A1127 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1147 removed outlier: 3.909A pdb=" N ILE A1138 " --> pdb=" O TRP A1134 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A1139 " --> pdb=" O PHE A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1155 removed outlier: 3.566A pdb=" N LEU A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 31 removed outlier: 4.633A pdb=" N GLY A 27 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 29 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU A 39 " --> pdb=" O CYS A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 129 removed outlier: 6.972A pdb=" N VAL A 122 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 142 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 124 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 140 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS A 126 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N GLN A 199 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA A 138 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASN A 201 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A 140 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LYS A 203 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 142 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 161 removed outlier: 4.215A pdb=" N GLY A 166 " --> pdb=" O PHE A 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 449 through 450 removed outlier: 3.507A pdb=" N THR A 508 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN A 396 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 937 through 938 removed outlier: 3.582A pdb=" N VAL A 938 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 946 " --> pdb=" O VAL A 938 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 870 through 872 433 hydrogen bonds defined for protein. 1245 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: 6.94 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8689 1.03 - 1.23: 162 1.23 - 1.43: 3782 1.43 - 1.63: 5331 1.63 - 1.82: 76 Bond restraints: 18040 Sorted by residual: bond pdb=" C13 Q7G A1202 " pdb=" C16 Q7G A1202 " ideal model delta sigma weight residual 1.509 1.336 0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C14 Q7G A1202 " pdb=" C15 Q7G A1202 " ideal model delta sigma weight residual 1.495 1.327 0.168 2.00e-02 2.50e+03 7.09e+01 bond pdb=" C13 Q7G A1202 " pdb=" C14 Q7G A1202 " ideal model delta sigma weight residual 1.333 1.465 -0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C07 Q7G A1202 " pdb=" C15 Q7G A1202 " ideal model delta sigma weight residual 1.528 1.485 0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C6 ERG A1201 " pdb=" C7 ERG A1201 " ideal model delta sigma weight residual 1.452 1.412 0.040 2.00e-02 2.50e+03 3.95e+00 ... (remaining 18035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 32439 3.45 - 6.91: 42 6.91 - 10.36: 4 10.36 - 13.81: 1 13.81 - 17.27: 4 Bond angle restraints: 32490 Sorted by residual: angle pdb=" O11 Q7G A1202 " pdb=" CF1 Q7G A1202 " pdb=" O51 Q7G A1202 " ideal model delta sigma weight residual 107.52 124.79 -17.27 3.00e+00 1.11e-01 3.31e+01 angle pdb=" O1 Q7G A1202 " pdb=" C1 Q7G A1202 " pdb=" O5 Q7G A1202 " ideal model delta sigma weight residual 107.91 124.97 -17.06 3.00e+00 1.11e-01 3.23e+01 angle pdb=" C5 Q7G A1202 " pdb=" C4 Q7G A1202 " pdb=" O4 Q7G A1202 " ideal model delta sigma weight residual 106.58 121.14 -14.56 3.00e+00 1.11e-01 2.36e+01 angle pdb=" C13 Q7G A1202 " pdb=" C16 Q7G A1202 " pdb=" C17 Q7G A1202 " ideal model delta sigma weight residual 111.45 125.29 -13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C2 ERG A1201 " pdb=" C3 ERG A1201 " pdb=" O1 ERG A1201 " ideal model delta sigma weight residual 108.67 121.69 -13.02 3.00e+00 1.11e-01 1.88e+01 ... (remaining 32485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.76: 8511 27.76 - 55.52: 432 55.52 - 83.28: 61 83.28 - 111.04: 18 111.04 - 138.80: 9 Dihedral angle restraints: 9031 sinusoidal: 5035 harmonic: 3996 Sorted by residual: dihedral pdb=" CB CYS A 868 " pdb=" SG CYS A 868 " pdb=" SG CYS A 925 " pdb=" CB CYS A 925 " ideal model delta sinusoidal sigma weight residual 93.00 160.22 -67.22 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS A 822 " pdb=" SG CYS A 822 " pdb=" SG CYS A 828 " pdb=" CB CYS A 828 " ideal model delta sinusoidal sigma weight residual -86.00 -37.41 -48.59 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 110 " pdb=" CB CYS A 110 " ideal model delta sinusoidal sigma weight residual -86.00 -132.72 46.72 1 1.00e+01 1.00e-02 3.02e+01 ... (remaining 9028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 1474 0.285 - 0.570: 0 0.570 - 0.854: 0 0.854 - 1.139: 0 1.139 - 1.424: 4 Chirality restraints: 1478 Sorted by residual: chirality pdb=" C4 Q7G A1202 " pdb=" C3 Q7G A1202 " pdb=" C5 Q7G A1202 " pdb=" O4 Q7G A1202 " both_signs ideal model delta sigma weight residual False -2.48 -1.06 -1.42 2.00e-01 2.50e+01 5.07e+01 chirality pdb=" C1 Q7G A1202 " pdb=" C2 Q7G A1202 " pdb=" O1 Q7G A1202 " pdb=" O5 Q7G A1202 " both_signs ideal model delta sigma weight residual False -2.31 -0.93 -1.38 2.00e-01 2.50e+01 4.75e+01 chirality pdb=" CF1 Q7G A1202 " pdb=" C21 Q7G A1202 " pdb=" O11 Q7G A1202 " pdb=" O51 Q7G A1202 " both_signs ideal model delta sigma weight residual False -2.32 -0.95 -1.37 2.00e-01 2.50e+01 4.68e+01 ... (remaining 1475 not shown) Planarity restraints: 2618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G A1202 " -0.018 2.00e-02 2.50e+03 6.03e-02 4.55e+01 pdb=" C13 Q7G A1202 " -0.014 2.00e-02 2.50e+03 pdb=" C14 Q7G A1202 " -0.096 2.00e-02 2.50e+03 pdb=" C15 Q7G A1202 " 0.076 2.00e-02 2.50e+03 pdb=" C16 Q7G A1202 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 686 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO A 687 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 687 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 687 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 954 " -0.017 5.00e-02 4.00e+02 2.53e-02 1.03e+00 pdb=" N PRO A 955 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 955 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 955 " -0.014 5.00e-02 4.00e+02 ... (remaining 2615 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1189 2.21 - 2.81: 36414 2.81 - 3.41: 46406 3.41 - 4.00: 60993 4.00 - 4.60: 94045 Nonbonded interactions: 239047 Sorted by model distance: nonbonded pdb=" HG SER A 547 " pdb=" OH TYR A 785 " model vdw 1.614 2.450 nonbonded pdb=" OE1 GLN A 214 " pdb=" H GLU A 215 " model vdw 1.640 2.450 nonbonded pdb=" HG1 THR A 845 " pdb=" OD2 ASP A 968 " model vdw 1.647 2.450 nonbonded pdb=" OE1 GLU A1101 " pdb=" H GLU A1101 " model vdw 1.665 2.450 nonbonded pdb=" O SER A 428 " pdb=" H ASN A 431 " model vdw 1.677 2.450 ... (remaining 239042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.130 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: 0.310 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.200 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.004 0.173 9363 Z= 0.201 Angle : 0.636 17.267 12765 Z= 0.273 Chirality : 0.082 1.424 1478 Planarity : 0.003 0.060 1565 Dihedral : 18.852 138.798 3822 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 0.10 % Allowed : 14.78 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.27), residues: 1095 helix: 0.74 (0.23), residues: 574 sheet: -0.66 (0.64), residues: 76 loop : -0.41 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 415 HIS 0.006 0.001 HIS A 954 PHE 0.010 0.001 PHE A 982 TYR 0.015 0.001 TYR A 565 ARG 0.001 0.000 ARG A 930 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 4) link_NAG-ASN : angle 1.52432 ( 12) link_BETA1-4 : bond 0.00302 ( 4) link_BETA1-4 : angle 2.21871 ( 12) hydrogen bonds : bond 0.26726 ( 433) hydrogen bonds : angle 8.15555 ( 1245) SS BOND : bond 0.00119 ( 14) SS BOND : angle 0.80470 ( 28) covalent geometry : bond 0.00423 ( 9341) covalent geometry : angle 0.63037 (12713) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.3884 time to fit residues: 56.4244 Evaluate side-chains 98 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 951 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN A 707 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.186091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124509 restraints weight = 30963.377| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.92 r_work: 0.3184 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9363 Z= 0.156 Angle : 0.602 8.740 12765 Z= 0.308 Chirality : 0.040 0.227 1478 Planarity : 0.003 0.026 1565 Dihedral : 13.583 106.535 1750 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 0.91 % Allowed : 13.87 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1095 helix: 1.03 (0.21), residues: 592 sheet: -0.48 (0.66), residues: 73 loop : -0.46 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 521 HIS 0.006 0.001 HIS A 954 PHE 0.018 0.001 PHE A 982 TYR 0.010 0.001 TYR A 565 ARG 0.001 0.000 ARG A 524 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 4) link_NAG-ASN : angle 1.44079 ( 12) link_BETA1-4 : bond 0.00335 ( 4) link_BETA1-4 : angle 1.42636 ( 12) hydrogen bonds : bond 0.07262 ( 433) hydrogen bonds : angle 5.42382 ( 1245) SS BOND : bond 0.00139 ( 14) SS BOND : angle 0.80558 ( 28) covalent geometry : bond 0.00338 ( 9341) covalent geometry : angle 0.59863 (12713) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8248 (tt0) cc_final: 0.7997 (tp40) REVERT: A 641 ASP cc_start: 0.7856 (m-30) cc_final: 0.7593 (m-30) REVERT: A 685 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8932 (m) outliers start: 9 outliers final: 5 residues processed: 102 average time/residue: 0.3791 time to fit residues: 57.6811 Evaluate side-chains 103 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 951 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN A 707 GLN A 959 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.182669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117130 restraints weight = 30789.573| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.79 r_work: 0.3107 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9363 Z= 0.161 Angle : 0.568 9.051 12765 Z= 0.285 Chirality : 0.040 0.314 1478 Planarity : 0.003 0.027 1565 Dihedral : 11.665 96.907 1750 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % Rotamer: Outliers : 1.11 % Allowed : 14.57 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1095 helix: 1.14 (0.22), residues: 594 sheet: -0.44 (0.66), residues: 73 loop : -0.55 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 521 HIS 0.006 0.001 HIS A 954 PHE 0.018 0.001 PHE A 982 TYR 0.007 0.001 TYR A 565 ARG 0.001 0.000 ARG A 750 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 4) link_NAG-ASN : angle 1.46806 ( 12) link_BETA1-4 : bond 0.00227 ( 4) link_BETA1-4 : angle 1.49908 ( 12) hydrogen bonds : bond 0.05981 ( 433) hydrogen bonds : angle 4.99553 ( 1245) SS BOND : bond 0.00136 ( 14) SS BOND : angle 0.85217 ( 28) covalent geometry : bond 0.00367 ( 9341) covalent geometry : angle 0.56423 (12713) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8146 (tt0) cc_final: 0.7867 (tp40) REVERT: A 641 ASP cc_start: 0.7747 (m-30) cc_final: 0.7466 (m-30) REVERT: A 685 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8907 (m) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.3674 time to fit residues: 59.2601 Evaluate side-chains 107 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1018 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.184050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118169 restraints weight = 30940.770| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.80 r_work: 0.2895 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9363 Z= 0.121 Angle : 0.546 8.346 12765 Z= 0.269 Chirality : 0.039 0.297 1478 Planarity : 0.003 0.029 1565 Dihedral : 10.417 86.474 1750 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 0.91 % Allowed : 15.38 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1095 helix: 1.27 (0.22), residues: 595 sheet: -0.39 (0.64), residues: 76 loop : -0.44 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 521 HIS 0.006 0.001 HIS A 954 PHE 0.016 0.001 PHE A 505 TYR 0.009 0.001 TYR A 179 ARG 0.001 0.000 ARG A 750 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 4) link_NAG-ASN : angle 1.32697 ( 12) link_BETA1-4 : bond 0.00245 ( 4) link_BETA1-4 : angle 1.43973 ( 12) hydrogen bonds : bond 0.04744 ( 433) hydrogen bonds : angle 4.67138 ( 1245) SS BOND : bond 0.00121 ( 14) SS BOND : angle 0.72270 ( 28) covalent geometry : bond 0.00274 ( 9341) covalent geometry : angle 0.54258 (12713) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.5705 (mmm) cc_final: 0.5289 (tpt) REVERT: A 332 GLN cc_start: 0.8029 (tt0) cc_final: 0.7737 (tp40) REVERT: A 568 MET cc_start: 0.7853 (tpp) cc_final: 0.7519 (tpp) REVERT: A 685 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8819 (m) REVERT: A 1112 PHE cc_start: 0.7951 (t80) cc_final: 0.7571 (t80) outliers start: 9 outliers final: 8 residues processed: 108 average time/residue: 0.3761 time to fit residues: 60.6602 Evaluate side-chains 113 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1078 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.183246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117861 restraints weight = 31102.639| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.84 r_work: 0.2903 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9363 Z= 0.133 Angle : 0.535 7.655 12765 Z= 0.264 Chirality : 0.039 0.334 1478 Planarity : 0.003 0.030 1565 Dihedral : 9.265 85.930 1750 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % Rotamer: Outliers : 1.52 % Allowed : 15.49 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1095 helix: 1.31 (0.22), residues: 597 sheet: -0.35 (0.65), residues: 72 loop : -0.48 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 415 HIS 0.006 0.001 HIS A 954 PHE 0.017 0.001 PHE A 982 TYR 0.008 0.001 TYR A 565 ARG 0.001 0.000 ARG A 750 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 4) link_NAG-ASN : angle 1.41668 ( 12) link_BETA1-4 : bond 0.00205 ( 4) link_BETA1-4 : angle 1.43323 ( 12) hydrogen bonds : bond 0.04383 ( 433) hydrogen bonds : angle 4.54646 ( 1245) SS BOND : bond 0.00118 ( 14) SS BOND : angle 0.77160 ( 28) covalent geometry : bond 0.00309 ( 9341) covalent geometry : angle 0.53139 (12713) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8021 (tt0) cc_final: 0.7738 (tp40) REVERT: A 685 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8806 (m) REVERT: A 1112 PHE cc_start: 0.7908 (t80) cc_final: 0.7551 (t80) outliers start: 15 outliers final: 11 residues processed: 116 average time/residue: 0.3952 time to fit residues: 68.8793 Evaluate side-chains 109 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1052 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.183568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117623 restraints weight = 31183.141| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.94 r_work: 0.2883 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9363 Z= 0.146 Angle : 0.539 7.681 12765 Z= 0.268 Chirality : 0.039 0.288 1478 Planarity : 0.003 0.030 1565 Dihedral : 8.876 84.554 1750 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 1.52 % Allowed : 16.40 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1095 helix: 1.31 (0.22), residues: 597 sheet: -0.36 (0.64), residues: 76 loop : -0.46 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 415 HIS 0.006 0.001 HIS A 954 PHE 0.018 0.001 PHE A 982 TYR 0.007 0.001 TYR A 179 ARG 0.001 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 4) link_NAG-ASN : angle 1.44361 ( 12) link_BETA1-4 : bond 0.00257 ( 4) link_BETA1-4 : angle 1.42745 ( 12) hydrogen bonds : bond 0.04255 ( 433) hydrogen bonds : angle 4.46575 ( 1245) SS BOND : bond 0.00139 ( 14) SS BOND : angle 0.82872 ( 28) covalent geometry : bond 0.00343 ( 9341) covalent geometry : angle 0.53554 (12713) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8089 (tt0) cc_final: 0.7785 (tp40) REVERT: A 1112 PHE cc_start: 0.7954 (t80) cc_final: 0.7614 (t80) outliers start: 15 outliers final: 12 residues processed: 109 average time/residue: 0.3689 time to fit residues: 59.7954 Evaluate side-chains 110 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1052 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 707 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.184965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117147 restraints weight = 31054.778| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.86 r_work: 0.2871 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9363 Z= 0.155 Angle : 0.544 7.631 12765 Z= 0.271 Chirality : 0.039 0.291 1478 Planarity : 0.003 0.030 1565 Dihedral : 8.786 85.480 1750 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.43 % Rotamer: Outliers : 1.32 % Allowed : 17.00 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1095 helix: 1.32 (0.22), residues: 597 sheet: -0.31 (0.65), residues: 72 loop : -0.49 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 415 HIS 0.006 0.001 HIS A 954 PHE 0.018 0.001 PHE A 982 TYR 0.007 0.001 TYR A 565 ARG 0.001 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 4) link_NAG-ASN : angle 1.49284 ( 12) link_BETA1-4 : bond 0.00220 ( 4) link_BETA1-4 : angle 1.41106 ( 12) hydrogen bonds : bond 0.04209 ( 433) hydrogen bonds : angle 4.45268 ( 1245) SS BOND : bond 0.00125 ( 14) SS BOND : angle 0.84991 ( 28) covalent geometry : bond 0.00366 ( 9341) covalent geometry : angle 0.53995 (12713) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8086 (tt0) cc_final: 0.7781 (tp40) REVERT: A 685 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8810 (m) REVERT: A 1112 PHE cc_start: 0.7916 (t80) cc_final: 0.7584 (t80) outliers start: 13 outliers final: 12 residues processed: 106 average time/residue: 0.3702 time to fit residues: 58.1385 Evaluate side-chains 110 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 707 GLN Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1052 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.185163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117542 restraints weight = 31035.103| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.88 r_work: 0.2892 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9363 Z= 0.124 Angle : 0.537 9.302 12765 Z= 0.267 Chirality : 0.039 0.282 1478 Planarity : 0.003 0.030 1565 Dihedral : 8.645 82.999 1750 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % Rotamer: Outliers : 1.11 % Allowed : 17.41 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1095 helix: 1.41 (0.22), residues: 591 sheet: -0.33 (0.64), residues: 76 loop : -0.35 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 415 HIS 0.005 0.001 HIS A 954 PHE 0.015 0.001 PHE A 982 TYR 0.006 0.001 TYR A 565 ARG 0.001 0.000 ARG A 750 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 4) link_NAG-ASN : angle 1.41516 ( 12) link_BETA1-4 : bond 0.00225 ( 4) link_BETA1-4 : angle 1.40661 ( 12) hydrogen bonds : bond 0.04096 ( 433) hydrogen bonds : angle 4.42375 ( 1245) SS BOND : bond 0.00117 ( 14) SS BOND : angle 0.73852 ( 28) covalent geometry : bond 0.00290 ( 9341) covalent geometry : angle 0.53296 (12713) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: A 332 GLN cc_start: 0.8054 (tt0) cc_final: 0.7751 (tp40) REVERT: A 641 ASP cc_start: 0.7749 (m-30) cc_final: 0.7477 (m-30) REVERT: A 1112 PHE cc_start: 0.7925 (t80) cc_final: 0.7600 (t80) outliers start: 11 outliers final: 10 residues processed: 106 average time/residue: 0.3764 time to fit residues: 59.3916 Evaluate side-chains 108 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 1052 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.183446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117624 restraints weight = 31030.656| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.81 r_work: 0.2875 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9363 Z= 0.116 Angle : 0.515 7.770 12765 Z= 0.257 Chirality : 0.038 0.269 1478 Planarity : 0.003 0.031 1565 Dihedral : 8.449 81.181 1750 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 1.32 % Allowed : 17.31 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1095 helix: 1.50 (0.22), residues: 592 sheet: -0.22 (0.65), residues: 72 loop : -0.32 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 415 HIS 0.005 0.001 HIS A 954 PHE 0.014 0.001 PHE A 505 TYR 0.006 0.001 TYR A 789 ARG 0.001 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 4) link_NAG-ASN : angle 1.33333 ( 12) link_BETA1-4 : bond 0.00266 ( 4) link_BETA1-4 : angle 1.38832 ( 12) hydrogen bonds : bond 0.03854 ( 433) hydrogen bonds : angle 4.34106 ( 1245) SS BOND : bond 0.00111 ( 14) SS BOND : angle 0.70411 ( 28) covalent geometry : bond 0.00268 ( 9341) covalent geometry : angle 0.51175 (12713) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 HIS cc_start: 0.8512 (m-70) cc_final: 0.8289 (m90) REVERT: A 332 GLN cc_start: 0.8043 (tt0) cc_final: 0.7758 (tp40) REVERT: A 563 ILE cc_start: 0.8531 (mm) cc_final: 0.8249 (mt) REVERT: A 640 TYR cc_start: 0.8167 (t80) cc_final: 0.7465 (t80) REVERT: A 1112 PHE cc_start: 0.7916 (t80) cc_final: 0.7643 (t80) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.3807 time to fit residues: 62.9083 Evaluate side-chains 108 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 707 GLN Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 1052 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 1.9990 chunk 72 optimal weight: 0.0370 chunk 85 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.184608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119003 restraints weight = 30925.239| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.88 r_work: 0.2911 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9363 Z= 0.100 Angle : 0.509 10.587 12765 Z= 0.253 Chirality : 0.038 0.258 1478 Planarity : 0.003 0.030 1565 Dihedral : 8.289 79.055 1750 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 1.11 % Allowed : 17.71 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.27), residues: 1095 helix: 1.58 (0.22), residues: 592 sheet: 0.03 (0.67), residues: 70 loop : -0.27 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 415 HIS 0.005 0.001 HIS A 954 PHE 0.019 0.001 PHE A 569 TYR 0.007 0.001 TYR A 789 ARG 0.001 0.000 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 4) link_NAG-ASN : angle 1.22962 ( 12) link_BETA1-4 : bond 0.00255 ( 4) link_BETA1-4 : angle 1.35381 ( 12) hydrogen bonds : bond 0.03632 ( 433) hydrogen bonds : angle 4.26945 ( 1245) SS BOND : bond 0.00102 ( 14) SS BOND : angle 0.62810 ( 28) covalent geometry : bond 0.00229 ( 9341) covalent geometry : angle 0.50621 (12713) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8018 (tt0) cc_final: 0.7739 (tp40) REVERT: A 563 ILE cc_start: 0.8546 (mm) cc_final: 0.8262 (mt) REVERT: A 1112 PHE cc_start: 0.7863 (t80) cc_final: 0.7592 (t80) outliers start: 11 outliers final: 9 residues processed: 107 average time/residue: 0.3735 time to fit residues: 59.8046 Evaluate side-chains 107 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 707 GLN Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1052 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.4980 chunk 3 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.183750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118250 restraints weight = 30942.027| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.84 r_work: 0.2915 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9363 Z= 0.123 Angle : 0.512 8.200 12765 Z= 0.255 Chirality : 0.039 0.260 1478 Planarity : 0.003 0.030 1565 Dihedral : 8.288 84.060 1750 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 1.21 % Allowed : 17.71 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1095 helix: 1.57 (0.22), residues: 592 sheet: -0.04 (0.66), residues: 70 loop : -0.30 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 415 HIS 0.005 0.001 HIS A 954 PHE 0.017 0.001 PHE A 569 TYR 0.005 0.001 TYR A 409 ARG 0.001 0.000 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 4) link_NAG-ASN : angle 1.34089 ( 12) link_BETA1-4 : bond 0.00211 ( 4) link_BETA1-4 : angle 1.33737 ( 12) hydrogen bonds : bond 0.03686 ( 433) hydrogen bonds : angle 4.25942 ( 1245) SS BOND : bond 0.00119 ( 14) SS BOND : angle 0.76904 ( 28) covalent geometry : bond 0.00290 ( 9341) covalent geometry : angle 0.50854 (12713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10550.69 seconds wall clock time: 180 minutes 59.65 seconds (10859.65 seconds total)