Starting phenix.real_space_refine on Tue May 13 10:53:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ox4_17256/05_2025/8ox4_17256.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ox4_17256/05_2025/8ox4_17256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ox4_17256/05_2025/8ox4_17256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ox4_17256/05_2025/8ox4_17256.map" model { file = "/net/cci-nas-00/data/ceres_data/8ox4_17256/05_2025/8ox4_17256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ox4_17256/05_2025/8ox4_17256.cif" } resolution = 3.4 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= -0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 6310 2.51 5 N 1610 2.21 5 O 1786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 9757 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 7015 Classifications: {'peptide': 870} Link IDs: {'PTRANS': 20, 'TRANS': 849} Chain breaks: 4 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.96, per 1000 atoms: 0.61 Number of scatterers: 9757 At special positions: 0 Unit cell: (87.992, 95.756, 170.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 3 15.00 Mg 1 11.99 O 1786 8.00 N 1610 7.00 C 6310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 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 C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 56.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.678A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 removed outlier: 3.601A pdb=" N ILE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 174 removed outlier: 3.503A pdb=" N VAL A 146 " --> pdb=" O TYR A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.726A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 366 removed outlier: 3.510A pdb=" N VAL A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 392 removed outlier: 3.840A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 400 removed outlier: 4.351A pdb=" N THR A 398 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 402 No H-bonds generated for 'chain 'A' and resid 401 through 402' Processing helix chain 'A' and resid 403 through 422 removed outlier: 4.008A pdb=" N GLU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 448 removed outlier: 4.033A pdb=" N ILE A 448 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 552 through 564 removed outlier: 3.750A pdb=" N ASN A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 removed outlier: 3.980A pdb=" N GLU A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 648 Processing helix chain 'A' and resid 662 through 677 removed outlier: 4.452A pdb=" N GLU A 668 " --> pdb=" O LYS A 664 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 669 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 682 through 695 removed outlier: 3.855A pdb=" N LEU A 687 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP A 688 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 removed outlier: 3.580A pdb=" N ALA A 724 " --> pdb=" O LYS A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 746 Processing helix chain 'A' and resid 757 through 773 Processing helix chain 'A' and resid 803 through 811 removed outlier: 3.576A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 858 Processing helix chain 'A' and resid 869 through 885 removed outlier: 3.674A pdb=" N VAL A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 897 through 904 removed outlier: 3.603A pdb=" N THR A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 930 No H-bonds generated for 'chain 'A' and resid 928 through 930' Processing helix chain 'A' and resid 931 through 938 removed outlier: 3.502A pdb=" N LEU A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 960 removed outlier: 4.033A pdb=" N TYR A 956 " --> pdb=" O ARG A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 969 removed outlier: 3.731A pdb=" N PHE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 973 removed outlier: 4.102A pdb=" N GLY A 973 " --> pdb=" O PHE A 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 970 through 973' Processing helix chain 'A' and resid 981 through 991 removed outlier: 3.982A pdb=" N THR A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 987 " --> pdb=" O TRP A 983 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 Processing helix chain 'A' and resid 1008 through 1014 Processing helix chain 'A' and resid 1015 through 1018 Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.592A pdb=" N GLN A1023 " --> pdb=" O TYR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1057 Proline residue: A1051 - end of helix removed outlier: 4.056A pdb=" N GLN A1057 " --> pdb=" O GLY A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1092 removed outlier: 3.795A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1118 removed outlier: 3.732A pdb=" N PHE A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1126 removed outlier: 3.696A pdb=" N HIS A1123 " --> pdb=" O SER A1119 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A1124 " --> pdb=" O ALA A1120 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU A1125 " --> pdb=" O GLY A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1140 removed outlier: 3.553A pdb=" N LEU A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1171 removed outlier: 3.527A pdb=" N TRP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS A1156 " --> pdb=" O THR A1152 " (cutoff:3.500A) Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1173 through 1181 removed outlier: 3.661A pdb=" N HIS A1181 " --> pdb=" O LYS A1177 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 75 removed outlier: 3.772A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.557A pdb=" N ILE B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Proline residue: B 63 - end of helix removed outlier: 3.654A pdb=" N ILE B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.793A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 171 through 177 removed outlier: 4.307A pdb=" N ALA B 175 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.639A pdb=" N ARG B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.841A pdb=" N MET B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B 243 " --> pdb=" O VAL B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 243' Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.514A pdb=" N ASP B 305 " --> pdb=" O HIS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 351 removed outlier: 3.659A pdb=" N GLY B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 426 through 427 removed outlier: 3.833A pdb=" N TYR A 427 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 801 through 802 removed outlier: 6.581A pdb=" N ILE A 801 " --> pdb=" O CYS A 866 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE A 728 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N CYS A 865 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 730 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE A 451 " --> pdb=" O TRP A 729 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU A 731 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N SER A 453 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 888 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A 908 " --> pdb=" O THR A 888 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA A 890 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.539A pdb=" N THR A 465 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE A 471 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU A 701 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 701 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 592 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.539A pdb=" N THR A 465 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE A 471 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU A 701 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 540 removed outlier: 3.546A pdb=" N MET A 538 " --> pdb=" O GLN A 549 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 567 through 572 removed outlier: 6.669A pdb=" N THR A 578 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1095 through 1096 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.842A pdb=" N VAL B 118 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU B 275 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET B 120 " --> pdb=" O TYR B 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 109 removed outlier: 4.108A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1347 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: 3.15 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3070 1.35 - 1.48: 2608 1.48 - 1.60: 4232 1.60 - 1.73: 4 1.73 - 1.86: 76 Bond restraints: 9990 Sorted by residual: bond pdb=" C1' ACP A1201 " pdb=" O4' ACP A1201 " ideal model delta sigma weight residual 1.390 1.618 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ACP A1201 " pdb=" C2' ACP A1201 " ideal model delta sigma weight residual 1.527 1.315 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C4' ACP A1201 " pdb=" O4' ACP A1201 " ideal model delta sigma weight residual 1.428 1.305 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C6 ACP A1201 " pdb=" N6 ACP A1201 " ideal model delta sigma weight residual 1.335 1.452 -0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C2' ACP A1201 " pdb=" O2' ACP A1201 " ideal model delta sigma weight residual 1.401 1.493 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 9985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 13469 3.05 - 6.09: 75 6.09 - 9.14: 7 9.14 - 12.19: 3 12.19 - 15.23: 3 Bond angle restraints: 13557 Sorted by residual: angle pdb=" O3A ACP A1201 " pdb=" PA ACP A1201 " pdb=" O5' ACP A1201 " ideal model delta sigma weight residual 93.75 108.98 -15.23 3.00e+00 1.11e-01 2.58e+01 angle pdb=" N1 ACP A1201 " pdb=" C6 ACP A1201 " pdb=" N6 ACP A1201 " ideal model delta sigma weight residual 119.32 104.55 14.77 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C5 ACP A1201 " pdb=" C6 ACP A1201 " pdb=" N6 ACP A1201 " ideal model delta sigma weight residual 122.65 135.47 -12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" C3B ACP A1201 " pdb=" PB ACP A1201 " pdb=" O3A ACP A1201 " ideal model delta sigma weight residual 98.05 109.44 -11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" O1B ACP A1201 " pdb=" PB ACP A1201 " pdb=" O2B ACP A1201 " ideal model delta sigma weight residual 119.60 109.44 10.16 3.00e+00 1.11e-01 1.15e+01 ... (remaining 13552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.56: 5817 33.56 - 67.12: 150 67.12 - 100.68: 16 100.68 - 134.24: 4 134.24 - 167.80: 1 Dihedral angle restraints: 5988 sinusoidal: 2480 harmonic: 3508 Sorted by residual: dihedral pdb=" O1A ACP A1201 " pdb=" O3A ACP A1201 " pdb=" PA ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sinusoidal sigma weight residual 311.25 143.45 167.80 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA PRO B 90 " pdb=" C PRO B 90 " pdb=" N CYS B 91 " pdb=" CA CYS B 91 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ILE A 463 " pdb=" C ILE A 463 " pdb=" N MET A 464 " pdb=" CA MET A 464 " ideal model delta harmonic sigma weight residual -180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1392 0.066 - 0.132: 125 0.132 - 0.198: 8 0.198 - 0.264: 1 0.264 - 0.330: 1 Chirality restraints: 1527 Sorted by residual: chirality pdb=" C2' ACP A1201 " pdb=" C1' ACP A1201 " pdb=" C3' ACP A1201 " pdb=" O2' ACP A1201 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ILE A 864 " pdb=" N ILE A 864 " pdb=" C ILE A 864 " pdb=" CB ILE A 864 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 1524 not shown) Planarity restraints: 1701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A1131 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C GLN A1131 " 0.038 2.00e-02 2.50e+03 pdb=" O GLN A1131 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A1132 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 169 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO B 170 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 195 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO B 196 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.024 5.00e-02 4.00e+02 ... (remaining 1698 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 65 2.50 - 3.10: 7405 3.10 - 3.70: 14750 3.70 - 4.30: 22555 4.30 - 4.90: 37160 Nonbonded interactions: 81935 Sorted by model distance: nonbonded pdb=" O LEU A 441 " pdb=" OH TYR A 924 " model vdw 1.898 3.040 nonbonded pdb=" OD2 ASP A 454 " pdb="MG MG A1202 " model vdw 1.947 2.170 nonbonded pdb=" O THR A 978 " pdb=" OH TYR A1069 " model vdw 1.988 3.040 nonbonded pdb=" O VAL A 990 " pdb=" OG SER A 994 " model vdw 2.046 3.040 nonbonded pdb=" O THR A 635 " pdb=" OG1 THR A 639 " model vdw 2.057 3.040 ... (remaining 81930 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.730 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 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 : 0.005 0.228 9998 Z= 0.235 Angle : 0.615 15.233 13578 Z= 0.288 Chirality : 0.040 0.330 1527 Planarity : 0.004 0.047 1698 Dihedral : 15.727 167.799 3721 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.65 (0.25), residues: 1186 helix: -0.18 (0.22), residues: 565 sheet: 0.35 (0.47), residues: 131 loop : -0.80 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1171 HIS 0.003 0.001 HIS A 535 PHE 0.011 0.001 PHE A1132 TYR 0.012 0.001 TYR A 427 ARG 0.003 0.000 ARG A 602 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 3) link_NAG-ASN : angle 1.27202 ( 9) link_BETA1-4 : bond 0.01166 ( 2) link_BETA1-4 : angle 2.73507 ( 6) hydrogen bonds : bond 0.24929 ( 466) hydrogen bonds : angle 8.83843 ( 1347) SS BOND : bond 0.00558 ( 3) SS BOND : angle 1.25635 ( 6) covalent geometry : bond 0.00492 ( 9990) covalent geometry : angle 0.61102 (13557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 CYS cc_start: 0.7910 (t) cc_final: 0.6926 (t) REVERT: A 535 HIS cc_start: 0.8220 (p-80) cc_final: 0.7454 (p-80) REVERT: A 654 LEU cc_start: 0.6891 (mp) cc_final: 0.6538 (mp) REVERT: A 799 LEU cc_start: 0.8033 (mp) cc_final: 0.7535 (tt) REVERT: A 864 ILE cc_start: 0.7763 (mm) cc_final: 0.7477 (mm) REVERT: B 29 ASP cc_start: 0.6342 (t0) cc_final: 0.6072 (t70) REVERT: B 45 LEU cc_start: 0.7526 (mt) cc_final: 0.7264 (mt) REVERT: B 79 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7143 (mt-10) REVERT: B 277 GLU cc_start: 0.5944 (mt-10) cc_final: 0.5718 (mt-10) REVERT: B 310 MET cc_start: 0.8072 (tmm) cc_final: 0.7774 (tmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2348 time to fit residues: 43.9726 Evaluate side-chains 114 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.2980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.0050 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS A 526 GLN A 741 ASN A1138 ASN B 254 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.239678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.231744 restraints weight = 9925.946| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 0.29 r_work: 0.4321 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.4219 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9998 Z= 0.159 Angle : 0.604 9.531 13578 Z= 0.311 Chirality : 0.043 0.238 1527 Planarity : 0.005 0.044 1698 Dihedral : 10.407 179.465 1442 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.57 % Allowed : 7.44 % Favored : 91.99 % 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: -0.21 (0.25), residues: 1186 helix: 0.33 (0.21), residues: 597 sheet: 0.37 (0.46), residues: 146 loop : -0.83 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1171 HIS 0.005 0.001 HIS A 939 PHE 0.029 0.002 PHE A 113 TYR 0.013 0.001 TYR A 924 ARG 0.003 0.000 ARG A 412 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 3) link_NAG-ASN : angle 1.35060 ( 9) link_BETA1-4 : bond 0.01897 ( 2) link_BETA1-4 : angle 3.03409 ( 6) hydrogen bonds : bond 0.04942 ( 466) hydrogen bonds : angle 5.67088 ( 1347) SS BOND : bond 0.00309 ( 3) SS BOND : angle 1.09711 ( 6) covalent geometry : bond 0.00366 ( 9990) covalent geometry : angle 0.59973 (13557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 875 MET cc_start: 0.7718 (ttp) cc_final: 0.7296 (ttt) REVERT: B 79 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7463 (mt-10) outliers start: 6 outliers final: 2 residues processed: 125 average time/residue: 0.2092 time to fit residues: 37.9799 Evaluate side-chains 109 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 439 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 73 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS ** A 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.236567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.227337 restraints weight = 9945.075| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 0.35 r_work: 0.4296 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.4217 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9998 Z= 0.156 Angle : 0.564 9.488 13578 Z= 0.286 Chirality : 0.042 0.251 1527 Planarity : 0.004 0.037 1698 Dihedral : 9.148 172.425 1442 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.24 % Allowed : 10.01 % Favored : 88.75 % 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: -0.09 (0.25), residues: 1186 helix: 0.52 (0.22), residues: 593 sheet: 0.31 (0.45), residues: 151 loop : -0.86 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1171 HIS 0.009 0.001 HIS A 535 PHE 0.023 0.002 PHE A 113 TYR 0.012 0.001 TYR A 924 ARG 0.003 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 3) link_NAG-ASN : angle 1.50646 ( 9) link_BETA1-4 : bond 0.01750 ( 2) link_BETA1-4 : angle 3.13584 ( 6) hydrogen bonds : bond 0.04376 ( 466) hydrogen bonds : angle 5.26954 ( 1347) SS BOND : bond 0.00344 ( 3) SS BOND : angle 1.05428 ( 6) covalent geometry : bond 0.00372 ( 9990) covalent geometry : angle 0.55867 (13557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 448 ILE cc_start: 0.9143 (mt) cc_final: 0.8938 (mt) REVERT: A 1131 GLN cc_start: 0.7506 (pp30) cc_final: 0.7009 (pt0) REVERT: B 45 LEU cc_start: 0.7681 (mt) cc_final: 0.7474 (mt) outliers start: 13 outliers final: 7 residues processed: 125 average time/residue: 0.2023 time to fit residues: 37.0092 Evaluate side-chains 118 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 59 optimal weight: 0.0070 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN A1087 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.239886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.229817 restraints weight = 9983.503| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 0.39 r_work: 0.4294 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.4187 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9998 Z= 0.142 Angle : 0.540 9.542 13578 Z= 0.274 Chirality : 0.041 0.252 1527 Planarity : 0.004 0.037 1698 Dihedral : 8.350 163.391 1442 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.72 % Allowed : 11.44 % Favored : 86.84 % 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: 0.00 (0.25), residues: 1186 helix: 0.63 (0.22), residues: 600 sheet: 0.41 (0.45), residues: 147 loop : -0.92 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1171 HIS 0.010 0.001 HIS A 535 PHE 0.026 0.001 PHE A 646 TYR 0.012 0.001 TYR A 924 ARG 0.005 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 3) link_NAG-ASN : angle 1.50914 ( 9) link_BETA1-4 : bond 0.01903 ( 2) link_BETA1-4 : angle 3.20534 ( 6) hydrogen bonds : bond 0.03918 ( 466) hydrogen bonds : angle 4.99927 ( 1347) SS BOND : bond 0.00288 ( 3) SS BOND : angle 1.02673 ( 6) covalent geometry : bond 0.00338 ( 9990) covalent geometry : angle 0.53389 (13557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.4872 (tpt) cc_final: 0.4605 (tpp) REVERT: A 397 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.7904 (p0) REVERT: A 1131 GLN cc_start: 0.7457 (pp30) cc_final: 0.7114 (pt0) REVERT: B 45 LEU cc_start: 0.7733 (mt) cc_final: 0.7091 (mt) REVERT: B 79 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7412 (mt-10) outliers start: 18 outliers final: 10 residues processed: 133 average time/residue: 0.2011 time to fit residues: 38.8997 Evaluate side-chains 118 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 51 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1087 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.235004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.225102 restraints weight = 9862.733| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 0.37 r_work: 0.4266 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.4183 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9998 Z= 0.190 Angle : 0.576 9.569 13578 Z= 0.291 Chirality : 0.042 0.251 1527 Planarity : 0.004 0.040 1698 Dihedral : 8.130 153.915 1442 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.10 % Allowed : 12.77 % Favored : 85.13 % 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: -0.11 (0.25), residues: 1186 helix: 0.54 (0.22), residues: 599 sheet: 0.39 (0.45), residues: 147 loop : -0.99 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1171 HIS 0.007 0.001 HIS A 535 PHE 0.028 0.002 PHE A 646 TYR 0.013 0.001 TYR B 122 ARG 0.005 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 3) link_NAG-ASN : angle 1.52585 ( 9) link_BETA1-4 : bond 0.01855 ( 2) link_BETA1-4 : angle 3.52904 ( 6) hydrogen bonds : bond 0.04071 ( 466) hydrogen bonds : angle 5.01571 ( 1347) SS BOND : bond 0.00295 ( 3) SS BOND : angle 1.16417 ( 6) covalent geometry : bond 0.00467 ( 9990) covalent geometry : angle 0.56986 (13557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.7958 (p0) REVERT: A 1055 TYR cc_start: 0.8289 (m-80) cc_final: 0.8047 (m-80) REVERT: A 1087 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7874 (tm130) REVERT: A 1104 PHE cc_start: 0.7951 (m-10) cc_final: 0.7678 (m-10) REVERT: A 1131 GLN cc_start: 0.7418 (pp30) cc_final: 0.7041 (pt0) REVERT: B 45 LEU cc_start: 0.7782 (mt) cc_final: 0.7126 (mt) outliers start: 22 outliers final: 15 residues processed: 126 average time/residue: 0.1975 time to fit residues: 36.1043 Evaluate side-chains 121 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 104 optimal weight: 0.0170 chunk 41 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1087 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.240813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.207340 restraints weight = 9906.836| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 1.11 r_work: 0.4038 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9998 Z= 0.121 Angle : 0.525 9.547 13578 Z= 0.265 Chirality : 0.040 0.252 1527 Planarity : 0.004 0.037 1698 Dihedral : 7.882 146.421 1442 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.53 % Allowed : 14.30 % Favored : 84.18 % 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: 0.08 (0.25), residues: 1186 helix: 0.72 (0.22), residues: 601 sheet: 0.54 (0.46), residues: 145 loop : -0.98 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1171 HIS 0.004 0.001 HIS A1118 PHE 0.023 0.001 PHE A 646 TYR 0.012 0.001 TYR A 924 ARG 0.006 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 3) link_NAG-ASN : angle 1.49581 ( 9) link_BETA1-4 : bond 0.01830 ( 2) link_BETA1-4 : angle 3.30923 ( 6) hydrogen bonds : bond 0.03643 ( 466) hydrogen bonds : angle 4.85437 ( 1347) SS BOND : bond 0.00254 ( 3) SS BOND : angle 0.94334 ( 6) covalent geometry : bond 0.00279 ( 9990) covalent geometry : angle 0.51887 (13557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.7952 (p0) REVERT: A 1104 PHE cc_start: 0.8021 (m-10) cc_final: 0.7786 (m-10) REVERT: A 1131 GLN cc_start: 0.7589 (pp30) cc_final: 0.7119 (pt0) REVERT: B 45 LEU cc_start: 0.7770 (mt) cc_final: 0.7116 (mt) outliers start: 16 outliers final: 11 residues processed: 118 average time/residue: 0.1913 time to fit residues: 33.0590 Evaluate side-chains 114 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 GLN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.234344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.226770 restraints weight = 10040.957| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 0.30 r_work: 0.4293 rms_B_bonded: 0.98 restraints_weight: 0.5000 r_work: 0.4197 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 9998 Z= 0.271 Angle : 0.642 9.643 13578 Z= 0.325 Chirality : 0.045 0.250 1527 Planarity : 0.004 0.043 1698 Dihedral : 7.845 131.569 1442 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.00 % Allowed : 14.78 % Favored : 83.22 % 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: -0.31 (0.25), residues: 1186 helix: 0.34 (0.22), residues: 600 sheet: 0.47 (0.44), residues: 146 loop : -1.10 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1171 HIS 0.007 0.001 HIS A 449 PHE 0.022 0.002 PHE A1048 TYR 0.019 0.002 TYR B 122 ARG 0.006 0.001 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 3) link_NAG-ASN : angle 1.53721 ( 9) link_BETA1-4 : bond 0.01935 ( 2) link_BETA1-4 : angle 3.91853 ( 6) hydrogen bonds : bond 0.04418 ( 466) hydrogen bonds : angle 5.07592 ( 1347) SS BOND : bond 0.00301 ( 3) SS BOND : angle 1.45685 ( 6) covalent geometry : bond 0.00670 ( 9990) covalent geometry : angle 0.63560 (13557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.7916 (p0) REVERT: A 1055 TYR cc_start: 0.8346 (m-80) cc_final: 0.8046 (m-80) REVERT: A 1104 PHE cc_start: 0.8020 (m-10) cc_final: 0.7748 (m-10) REVERT: A 1131 GLN cc_start: 0.7521 (pp30) cc_final: 0.7188 (pt0) REVERT: B 45 LEU cc_start: 0.7823 (mt) cc_final: 0.7158 (mt) REVERT: B 318 MET cc_start: 0.3685 (tpp) cc_final: 0.3475 (tpp) outliers start: 21 outliers final: 15 residues processed: 126 average time/residue: 0.2112 time to fit residues: 39.1396 Evaluate side-chains 125 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 109 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.238973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.195641 restraints weight = 10030.955| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.60 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9998 Z= 0.128 Angle : 0.545 9.459 13578 Z= 0.273 Chirality : 0.041 0.248 1527 Planarity : 0.004 0.038 1698 Dihedral : 7.680 127.806 1442 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.53 % Allowed : 15.73 % Favored : 82.75 % 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: -0.00 (0.25), residues: 1186 helix: 0.63 (0.22), residues: 601 sheet: 0.57 (0.46), residues: 146 loop : -1.00 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1171 HIS 0.005 0.001 HIS A 535 PHE 0.019 0.001 PHE A 646 TYR 0.012 0.001 TYR A 924 ARG 0.004 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00046 ( 3) link_NAG-ASN : angle 1.49675 ( 9) link_BETA1-4 : bond 0.01866 ( 2) link_BETA1-4 : angle 3.42143 ( 6) hydrogen bonds : bond 0.03684 ( 466) hydrogen bonds : angle 4.80989 ( 1347) SS BOND : bond 0.00274 ( 3) SS BOND : angle 0.98479 ( 6) covalent geometry : bond 0.00302 ( 9990) covalent geometry : angle 0.53920 (13557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.7889 (p0) REVERT: A 1055 TYR cc_start: 0.8065 (m-80) cc_final: 0.7845 (m-80) REVERT: A 1104 PHE cc_start: 0.7890 (m-10) cc_final: 0.7610 (m-10) REVERT: A 1131 GLN cc_start: 0.7436 (pp30) cc_final: 0.6918 (pt0) REVERT: B 45 LEU cc_start: 0.7727 (mt) cc_final: 0.7050 (mt) outliers start: 16 outliers final: 11 residues processed: 128 average time/residue: 0.2028 time to fit residues: 37.4785 Evaluate side-chains 125 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 6 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.236816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.181253 restraints weight = 9870.662| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.50 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9998 Z= 0.134 Angle : 0.543 9.527 13578 Z= 0.274 Chirality : 0.041 0.253 1527 Planarity : 0.004 0.039 1698 Dihedral : 7.595 123.880 1442 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.81 % Allowed : 16.21 % Favored : 81.98 % 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: 0.07 (0.25), residues: 1186 helix: 0.71 (0.22), residues: 599 sheet: 0.56 (0.46), residues: 147 loop : -0.98 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A1171 HIS 0.005 0.001 HIS A 535 PHE 0.018 0.001 PHE A 646 TYR 0.010 0.001 TYR A 924 ARG 0.004 0.000 ARG B 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 3) link_NAG-ASN : angle 1.52954 ( 9) link_BETA1-4 : bond 0.01817 ( 2) link_BETA1-4 : angle 3.37199 ( 6) hydrogen bonds : bond 0.03636 ( 466) hydrogen bonds : angle 4.76947 ( 1347) SS BOND : bond 0.00233 ( 3) SS BOND : angle 1.00393 ( 6) covalent geometry : bond 0.00323 ( 9990) covalent geometry : angle 0.53737 (13557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.7841 (p0) REVERT: A 535 HIS cc_start: 0.8505 (p-80) cc_final: 0.7770 (p-80) REVERT: A 554 ASP cc_start: 0.8129 (t0) cc_final: 0.7734 (t0) REVERT: A 648 ASN cc_start: 0.7432 (t0) cc_final: 0.6979 (m110) REVERT: A 799 LEU cc_start: 0.7983 (tt) cc_final: 0.7679 (tt) REVERT: A 1000 MET cc_start: 0.7953 (ttp) cc_final: 0.7749 (ttm) REVERT: A 1055 TYR cc_start: 0.8036 (m-80) cc_final: 0.7788 (m-80) REVERT: A 1104 PHE cc_start: 0.7851 (m-10) cc_final: 0.7543 (m-10) REVERT: A 1131 GLN cc_start: 0.7439 (pp30) cc_final: 0.6816 (pt0) REVERT: B 292 SER cc_start: 0.7939 (p) cc_final: 0.7698 (m) REVERT: B 310 MET cc_start: 0.7956 (tmm) cc_final: 0.7683 (tmm) outliers start: 19 outliers final: 14 residues processed: 129 average time/residue: 0.1953 time to fit residues: 37.0512 Evaluate side-chains 125 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 17 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 108 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.4492 r_free = 0.4492 target = 0.239821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.182501 restraints weight = 10050.575| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 4.12 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9998 Z= 0.127 Angle : 0.540 9.581 13578 Z= 0.272 Chirality : 0.040 0.256 1527 Planarity : 0.004 0.038 1698 Dihedral : 7.525 120.389 1442 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.53 % Allowed : 16.78 % Favored : 81.70 % 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: 0.11 (0.25), residues: 1186 helix: 0.75 (0.22), residues: 599 sheet: 0.58 (0.46), residues: 147 loop : -0.97 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1171 HIS 0.005 0.001 HIS A 535 PHE 0.018 0.001 PHE A 646 TYR 0.011 0.001 TYR B 121 ARG 0.007 0.000 ARG B 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 3) link_NAG-ASN : angle 1.53833 ( 9) link_BETA1-4 : bond 0.01858 ( 2) link_BETA1-4 : angle 3.25695 ( 6) hydrogen bonds : bond 0.03535 ( 466) hydrogen bonds : angle 4.71851 ( 1347) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.94440 ( 6) covalent geometry : bond 0.00303 ( 9990) covalent geometry : angle 0.53451 (13557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7674 (p0) REVERT: A 535 HIS cc_start: 0.8317 (p-80) cc_final: 0.7887 (p-80) REVERT: A 648 ASN cc_start: 0.7342 (t0) cc_final: 0.7099 (m110) REVERT: A 799 LEU cc_start: 0.7870 (tt) cc_final: 0.7546 (tt) REVERT: A 1000 MET cc_start: 0.7955 (ttp) cc_final: 0.7738 (ttm) REVERT: A 1055 TYR cc_start: 0.8090 (m-80) cc_final: 0.7886 (m-80) REVERT: A 1104 PHE cc_start: 0.7816 (m-10) cc_final: 0.7527 (m-10) REVERT: A 1131 GLN cc_start: 0.7700 (pp30) cc_final: 0.7151 (pt0) REVERT: B 45 LEU cc_start: 0.7796 (mt) cc_final: 0.7187 (mt) outliers start: 16 outliers final: 13 residues processed: 124 average time/residue: 0.1972 time to fit residues: 35.9112 Evaluate side-chains 121 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 106 optimal weight: 0.0670 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.235298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.183179 restraints weight = 9867.185| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.78 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9998 Z= 0.174 Angle : 0.571 9.548 13578 Z= 0.289 Chirality : 0.042 0.253 1527 Planarity : 0.004 0.040 1698 Dihedral : 7.568 115.758 1442 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.53 % Allowed : 17.16 % Favored : 81.32 % 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: -0.01 (0.25), residues: 1186 helix: 0.64 (0.22), residues: 599 sheet: 0.53 (0.46), residues: 147 loop : -1.01 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1171 HIS 0.005 0.001 HIS A 535 PHE 0.035 0.002 PHE A 646 TYR 0.014 0.001 TYR B 122 ARG 0.007 0.000 ARG B 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 3) link_NAG-ASN : angle 1.53659 ( 9) link_BETA1-4 : bond 0.01684 ( 2) link_BETA1-4 : angle 3.37209 ( 6) hydrogen bonds : bond 0.03793 ( 466) hydrogen bonds : angle 4.79600 ( 1347) SS BOND : bond 0.00223 ( 3) SS BOND : angle 1.11976 ( 6) covalent geometry : bond 0.00427 ( 9990) covalent geometry : angle 0.56546 (13557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3907.88 seconds wall clock time: 69 minutes 11.32 seconds (4151.32 seconds total)