Starting phenix.real_space_refine on Sat Sep 12 02:14:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7krp_23009/09_2026/7krp_23009.cif Found real_map, /net/cci-nas-00/data/ceres_data/7krp_23009/09_2026/7krp_23009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7krp_23009/09_2026/7krp_23009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7krp_23009/09_2026/7krp_23009.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7krp_23009/09_2026/7krp_23009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7krp_23009/09_2026/7krp_23009.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7krp_23009/09_2026/7krp_23009.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7krp_23009/09_2026/7krp_23009.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.093 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 75 5.49 5 Mg 1 5.21 5 S 83 5.16 5 C 7700 2.51 5 N 2111 2.21 5 O 2589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12561 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1416 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1427 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 776 Classifications: {'RNAv2': 37} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 36} Chain: "T" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 769 Classifications: {'RNAv2': 36} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 24.703 58.884 80.276 1.00 23.18 S ATOM 2495 SG CYS A 306 25.136 60.110 83.908 1.00 20.09 S ATOM 2527 SG CYS A 310 25.698 56.441 82.999 1.00 17.07 S ATOM 3935 SG CYS A 487 27.719 72.698 66.042 1.00 28.42 S ATOM 5188 SG CYS A 645 27.788 75.074 69.011 1.00 32.11 S ATOM 5194 SG CYS A 646 26.236 71.615 69.477 1.00 29.89 S Time building chain proxies: 2.76, per 1000 atoms: 0.22 Number of scatterers: 12561 At special positions: 0 Unit cell: (95.85, 161.88, 142.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 83 16.00 P 75 15.00 Mg 1 11.99 O 2589 8.00 N 2111 7.00 C 7700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 517.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 6 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 53.4% alpha, 11.3% beta 33 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.534A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.524A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.569A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.631A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.857A pdb=" N SER A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.529A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.954A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.566A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.763A pdb=" N TYR A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.487A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.640A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.518A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.955A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.649A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.162A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.566A pdb=" N ASN A 600 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 717 through 732 removed outlier: 3.717A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.580A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 808 removed outlier: 3.781A pdb=" N LYS A 807 " --> pdb=" O ASP A 804 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 808 " --> pdb=" O LEU A 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 804 through 808' Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.684A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 838 " --> pdb=" O PRO A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.625A pdb=" N ASP A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.054A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.214A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.757A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 97 removed outlier: 3.761A pdb=" N ARG B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 110 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 143 removed outlier: 4.091A pdb=" N ASP B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.733A pdb=" N VAL C 6 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.535A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.536A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 32 through 63 removed outlier: 3.744A pdb=" N MET D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 4.292A pdb=" N SER D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 99 removed outlier: 4.012A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.662A pdb=" N ASN D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.623A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.227A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.510A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.528A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.758A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 755 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 815 through 822 Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.437A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3662 1.34 - 1.46: 2591 1.46 - 1.57: 6398 1.57 - 1.69: 197 1.69 - 1.81: 130 Bond restraints: 12978 Sorted by residual: bond pdb=" C17 1N7 A1005 " pdb=" C18 1N7 A1005 " ideal model delta sigma weight residual 1.528 1.638 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C17 1N7 D 201 " pdb=" C18 1N7 D 201 " ideal model delta sigma weight residual 1.528 1.633 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C17 1N7 A1006 " pdb=" C18 1N7 A1006 " ideal model delta sigma weight residual 1.528 1.630 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C24 1N7 A1005 " pdb=" N1 1N7 A1005 " ideal model delta sigma weight residual 1.346 1.441 -0.095 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C24 1N7 D 201 " pdb=" N1 1N7 D 201 " ideal model delta sigma weight residual 1.346 1.440 -0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 12973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 17603 2.42 - 4.84: 315 4.84 - 7.26: 40 7.26 - 9.68: 8 9.68 - 12.10: 1 Bond angle restraints: 17967 Sorted by residual: angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C3' C P 25 " pdb=" O3' C P 25 " pdb=" P U P 26 " ideal model delta sigma weight residual 119.70 124.58 -4.88 1.20e+00 6.94e-01 1.65e+01 angle pdb=" C4 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C9 1N7 A1005 " ideal model delta sigma weight residual 117.60 105.50 12.10 3.00e+00 1.11e-01 1.63e+01 angle pdb=" C23 1N7 A1005 " pdb=" C24 1N7 A1005 " pdb=" N1 1N7 A1005 " ideal model delta sigma weight residual 115.43 125.06 -9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C23 1N7 D 201 " pdb=" C24 1N7 D 201 " pdb=" N1 1N7 D 201 " ideal model delta sigma weight residual 115.43 125.03 -9.60 3.00e+00 1.11e-01 1.02e+01 ... (remaining 17962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.57: 7329 30.57 - 61.15: 239 61.15 - 91.72: 11 91.72 - 122.29: 0 122.29 - 152.87: 3 Dihedral angle restraints: 7582 sinusoidal: 3501 harmonic: 4081 Sorted by residual: dihedral pdb=" C4' C P 39 " pdb=" C3' C P 39 " pdb=" C2' C P 39 " pdb=" C1' C P 39 " ideal model delta sinusoidal sigma weight residual 36.34 -34.47 70.82 1 3.10e+00 1.04e-01 6.71e+02 dihedral pdb=" O4' C P 39 " pdb=" C4' C P 39 " pdb=" C3' C P 39 " pdb=" C2' C P 39 " ideal model delta sinusoidal sigma weight residual -35.15 20.91 -56.06 1 4.00e+00 6.25e-02 2.65e+02 dihedral pdb=" O4' C P 39 " pdb=" C2' C P 39 " pdb=" C1' C P 39 " pdb=" C3' C P 39 " ideal model delta sinusoidal sigma weight residual -94.41 -37.28 -57.13 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 7579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.025: 2099 1.025 - 2.051: 0 2.051 - 3.076: 0 3.076 - 4.101: 0 4.101 - 5.127: 2 Chirality restraints: 2101 Sorted by residual: chirality pdb=" C6 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C7 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.43 2.70 -5.13 2.00e-01 2.50e+01 6.57e+02 chirality pdb=" C18 1N7 A1005 " pdb=" C17 1N7 A1005 " pdb=" C19 1N7 A1005 " pdb=" C6 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.53 -2.56 5.09 2.00e-01 2.50e+01 6.48e+02 chirality pdb=" C17 1N7 A1006 " pdb=" C16 1N7 A1006 " pdb=" C18 1N7 A1006 " pdb=" O3 1N7 A1006 " both_signs ideal model delta sigma weight residual False 2.40 2.82 -0.42 2.00e-01 2.50e+01 4.37e+00 ... (remaining 2098 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 338 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO A 339 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 93 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO A 94 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 338 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C VAL A 338 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL A 338 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO A 339 " -0.009 2.00e-02 2.50e+03 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 37 2.41 - 3.03: 7122 3.03 - 3.65: 19487 3.65 - 4.28: 29473 4.28 - 4.90: 48399 Nonbonded interactions: 104518 Sorted by model distance: nonbonded pdb="MG MG A1003 " pdb=" O2A ADP A1004 " model vdw 1.784 2.170 nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1003 " model vdw 2.048 2.170 nonbonded pdb=" OD2 ASP A 218 " pdb="MG MG A1003 " model vdw 2.065 2.170 nonbonded pdb="MG MG A1003 " pdb=" O1B ADP A1004 " model vdw 2.074 2.170 nonbonded pdb=" O TYR A 915 " pdb=" OH TYR A 921 " model vdw 2.227 3.040 ... (remaining 104513 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' and resid 7 through 191) selection = (chain 'D' and (resid 7 through 19 or (resid 20 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 23 or (resid 24 through \ 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 31 or (resid 32 and (name N or name CA or name C or name O or name CB )) or resi \ d 33 through 38 or (resid 39 and (name N or name CA or name C or name O or name \ CB )) or resid 40 through 191)) } 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.930 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 12986 Z= 0.300 Angle : 0.745 12.105 17973 Z= 0.381 Chirality : 0.171 5.127 2101 Planarity : 0.003 0.042 2007 Dihedral : 13.947 152.867 4940 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.18 % Allowed : 6.95 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.22), residues: 1365 helix: -0.49 (0.20), residues: 672 sheet: -1.31 (0.44), residues: 136 loop : -1.41 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 726 TYR 0.014 0.001 TYR A 788 PHE 0.013 0.002 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.30 (12978) covalent geometry : angle 0.74467 / 0.38 (17967) hydrogen bonds : bond 0.14086 / 9.47 ( 631) hydrogen bonds : angle 5.95361 / 4.12 ( 1707) metal coordination : bond 0.00630 / 0.33 ( 8) metal coordination : angle 1.60078 / 1.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 344 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.7637 (m-10) cc_final: 0.7386 (m-10) REVERT: A 450 ILE cc_start: 0.7101 (tp) cc_final: 0.6844 (tp) REVERT: A 481 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6739 (t0) REVERT: A 666 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.5429 (mtt) REVERT: A 755 MET cc_start: 0.6677 (ttm) cc_final: 0.6449 (ttp) REVERT: A 768 SER cc_start: 0.5726 (m) cc_final: 0.5466 (m) REVERT: B 165 LYS cc_start: 0.5807 (mptt) cc_final: 0.5396 (tmtt) REVERT: D 176 ASN cc_start: 0.5391 (OUTLIER) cc_final: 0.4997 (t0) outliers start: 50 outliers final: 13 residues processed: 379 average time/residue: 0.1027 time to fit residues: 56.3453 Evaluate side-chains 228 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 113 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 613 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126612 restraints weight = 14836.827| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.41 r_work: 0.3431 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 12986 Z= 0.219 Angle : 0.787 14.303 17973 Z= 0.372 Chirality : 0.052 0.613 2101 Planarity : 0.005 0.068 2007 Dihedral : 10.819 162.824 2419 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.18 % Allowed : 13.56 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.22), residues: 1365 helix: 0.07 (0.20), residues: 696 sheet: -1.20 (0.45), residues: 129 loop : -1.40 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 750 TYR 0.025 0.002 TYR A 32 PHE 0.019 0.002 PHE D 92 TRP 0.025 0.002 TRP D 182 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (12978) covalent geometry : angle 0.78574 / 0.37 (17967) hydrogen bonds : bond 0.04301 / 2.85 ( 631) hydrogen bonds : angle 4.38265 / 3.04 ( 1707) metal coordination : bond 0.00965 / 0.49 ( 8) metal coordination : angle 2.09636 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8296 (p0) cc_final: 0.7991 (p0) REVERT: A 235 ASP cc_start: 0.7705 (m-30) cc_final: 0.6938 (p0) REVERT: A 481 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7978 (t0) REVERT: A 703 ASN cc_start: 0.8518 (m110) cc_final: 0.8282 (m110) REVERT: A 722 ASN cc_start: 0.7897 (t0) cc_final: 0.7247 (m-40) REVERT: A 911 ASN cc_start: 0.7818 (p0) cc_final: 0.7603 (p0) REVERT: B 70 MET cc_start: 0.6447 (tpp) cc_final: 0.6074 (ttm) REVERT: B 136 ASN cc_start: 0.6160 (m110) cc_final: 0.5877 (m-40) REVERT: B 165 LYS cc_start: 0.6604 (mptt) cc_final: 0.6330 (mptt) REVERT: C 23 GLU cc_start: 0.8028 (tt0) cc_final: 0.7755 (tt0) REVERT: D 62 MET cc_start: 0.6920 (tpp) cc_final: 0.6630 (ttm) REVERT: D 78 ASP cc_start: 0.6667 (t70) cc_final: 0.6281 (t0) outliers start: 38 outliers final: 21 residues processed: 251 average time/residue: 0.0810 time to fit residues: 31.8086 Evaluate side-chains 205 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 48 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN A 312 ASN A 497 ASN A 613 HIS A 703 ASN A 789 GLN B 157 GLN D 65 GLN D 100 ASN D 176 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.151152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114741 restraints weight = 14979.522| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.68 r_work: 0.3284 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 12986 Z= 0.196 Angle : 0.677 10.808 17973 Z= 0.330 Chirality : 0.049 0.460 2101 Planarity : 0.004 0.061 2007 Dihedral : 10.519 176.056 2407 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.51 % Allowed : 15.48 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.22), residues: 1365 helix: 0.43 (0.20), residues: 696 sheet: -1.11 (0.45), residues: 124 loop : -1.35 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 889 TYR 0.015 0.002 TYR A 515 PHE 0.021 0.002 PHE D 92 TRP 0.010 0.001 TRP A 916 HIS 0.022 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (12978) covalent geometry : angle 0.67483 / 0.33 (17967) hydrogen bonds : bond 0.03999 / 2.62 ( 631) hydrogen bonds : angle 4.18693 / 2.92 ( 1707) metal coordination : bond 0.07128 / 3.75 ( 8) metal coordination : angle 3.20016 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.278 Fit side-chains REVERT: A 121 LYS cc_start: 0.7657 (tttt) cc_final: 0.7288 (ttpp) REVERT: A 221 ASP cc_start: 0.8194 (p0) cc_final: 0.7838 (p0) REVERT: A 235 ASP cc_start: 0.7848 (m-30) cc_final: 0.6983 (p0) REVERT: A 246 THR cc_start: 0.8102 (p) cc_final: 0.7883 (p) REVERT: A 431 GLU cc_start: 0.6923 (tp30) cc_final: 0.6408 (tp30) REVERT: A 441 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8486 (t80) REVERT: A 451 SER cc_start: 0.7446 (m) cc_final: 0.7201 (t) REVERT: A 551 LYS cc_start: 0.7488 (ptmm) cc_final: 0.7081 (mmtt) REVERT: A 668 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7487 (tmm) REVERT: A 718 LYS cc_start: 0.8117 (tptt) cc_final: 0.7856 (tptp) REVERT: A 722 ASN cc_start: 0.7788 (t0) cc_final: 0.7464 (t0) REVERT: A 828 TYR cc_start: 0.8907 (m-80) cc_final: 0.8671 (m-80) REVERT: A 857 GLU cc_start: 0.6978 (mp0) cc_final: 0.6594 (tp30) REVERT: A 913 SER cc_start: 0.8835 (t) cc_final: 0.8590 (m) REVERT: A 926 THR cc_start: 0.8455 (m) cc_final: 0.8053 (p) REVERT: B 90 MET cc_start: 0.7906 (tmm) cc_final: 0.7630 (ttm) REVERT: B 92 PHE cc_start: 0.6446 (m-80) cc_final: 0.6164 (m-80) REVERT: B 165 LYS cc_start: 0.6730 (mptt) cc_final: 0.5927 (tttm) REVERT: B 174 MET cc_start: 0.7568 (mmt) cc_final: 0.7030 (tpt) REVERT: C 18 GLN cc_start: 0.8580 (tm-30) cc_final: 0.7934 (tm-30) REVERT: D 50 ASP cc_start: 0.6721 (t0) cc_final: 0.5645 (m-30) REVERT: D 62 MET cc_start: 0.7205 (tpp) cc_final: 0.6828 (ttp) REVERT: D 70 MET cc_start: 0.7358 (tpp) cc_final: 0.7107 (mmm) REVERT: D 78 ASP cc_start: 0.6945 (t70) cc_final: 0.6562 (t0) REVERT: D 97 LYS cc_start: 0.8098 (tttm) cc_final: 0.7348 (mttt) REVERT: D 185 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.8004 (mt) outliers start: 42 outliers final: 19 residues processed: 193 average time/residue: 0.0905 time to fit residues: 26.9763 Evaluate side-chains 158 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 97 optimal weight: 8.9990 chunk 117 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114101 restraints weight = 14814.071| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.59 r_work: 0.3261 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.400 12986 Z= 0.166 Angle : 0.636 16.217 17973 Z= 0.296 Chirality : 0.045 0.328 2101 Planarity : 0.004 0.051 2007 Dihedral : 10.253 179.940 2398 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.35 % Allowed : 16.99 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.22), residues: 1365 helix: 0.64 (0.20), residues: 698 sheet: -1.00 (0.45), residues: 124 loop : -1.21 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.015 0.001 TYR A 515 PHE 0.015 0.001 PHE D 92 TRP 0.010 0.001 TRP A 916 HIS 0.049 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (12978) covalent geometry : angle 0.60833 / 0.29 (17967) hydrogen bonds : bond 0.03384 / 2.21 ( 631) hydrogen bonds : angle 3.96491 / 2.76 ( 1707) metal coordination : bond 0.14135 / 7.44 ( 8) metal coordination : angle 10.09156 / 4.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.346 Fit side-chains REVERT: A 221 ASP cc_start: 0.8230 (p0) cc_final: 0.7930 (p0) REVERT: A 235 ASP cc_start: 0.7975 (m-30) cc_final: 0.7130 (p0) REVERT: A 246 THR cc_start: 0.8284 (p) cc_final: 0.8073 (p) REVERT: A 431 GLU cc_start: 0.7129 (tp30) cc_final: 0.6762 (tp30) REVERT: A 441 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8639 (t80) REVERT: A 497 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7877 (t0) REVERT: A 551 LYS cc_start: 0.7523 (ptmm) cc_final: 0.7098 (mmtt) REVERT: A 608 ASP cc_start: 0.7592 (t0) cc_final: 0.7239 (t0) REVERT: A 718 LYS cc_start: 0.7917 (tptt) cc_final: 0.7666 (tptp) REVERT: A 722 ASN cc_start: 0.7784 (t0) cc_final: 0.7514 (t0) REVERT: A 750 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8172 (mmt90) REVERT: A 857 GLU cc_start: 0.7158 (mp0) cc_final: 0.6645 (tp30) REVERT: A 911 ASN cc_start: 0.7810 (p0) cc_final: 0.7609 (p0) REVERT: A 913 SER cc_start: 0.8856 (t) cc_final: 0.8563 (m) REVERT: A 926 THR cc_start: 0.8614 (m) cc_final: 0.8158 (p) REVERT: B 165 LYS cc_start: 0.7008 (mptt) cc_final: 0.6312 (tttm) REVERT: B 174 MET cc_start: 0.7671 (mmt) cc_final: 0.7149 (tpt) REVERT: D 50 ASP cc_start: 0.6698 (t0) cc_final: 0.5708 (m-30) REVERT: D 62 MET cc_start: 0.7174 (tpp) cc_final: 0.6794 (ttp) REVERT: D 70 MET cc_start: 0.7207 (tpp) cc_final: 0.6932 (mmm) REVERT: D 97 LYS cc_start: 0.8333 (tttm) cc_final: 0.8004 (ttmm) REVERT: D 164 SER cc_start: 0.7497 (m) cc_final: 0.6790 (t) REVERT: D 179 ASN cc_start: 0.5160 (m110) cc_final: 0.4740 (m-40) REVERT: D 185 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8018 (mt) outliers start: 40 outliers final: 21 residues processed: 175 average time/residue: 0.0980 time to fit residues: 26.3796 Evaluate side-chains 158 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 132 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111265 restraints weight = 14848.610| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.66 r_work: 0.3231 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.7924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 12986 Z= 0.163 Angle : 0.616 9.148 17973 Z= 0.293 Chirality : 0.046 0.322 2101 Planarity : 0.004 0.051 2007 Dihedral : 10.106 170.428 2398 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.85 % Allowed : 16.15 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.22), residues: 1365 helix: 0.77 (0.20), residues: 697 sheet: -0.91 (0.45), residues: 124 loop : -1.18 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.019 0.001 TYR A 294 PHE 0.016 0.001 PHE A 415 TRP 0.012 0.001 TRP D 182 HIS 0.015 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (12978) covalent geometry : angle 0.61094 / 0.29 (17967) hydrogen bonds : bond 0.03441 / 2.26 ( 631) hydrogen bonds : angle 3.89578 / 2.72 ( 1707) metal coordination : bond 0.05387 / 2.84 ( 8) metal coordination : angle 4.31551 / 1.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 0.392 Fit side-chains REVERT: A 40 ASP cc_start: 0.8235 (m-30) cc_final: 0.7788 (p0) REVERT: A 235 ASP cc_start: 0.7934 (m-30) cc_final: 0.7117 (p0) REVERT: A 268 TRP cc_start: 0.8073 (OUTLIER) cc_final: 0.5229 (m-90) REVERT: A 404 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8176 (p0) REVERT: A 431 GLU cc_start: 0.7162 (tp30) cc_final: 0.6937 (tp30) REVERT: A 441 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8523 (t80) REVERT: A 533 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.8034 (mtp85) REVERT: A 551 LYS cc_start: 0.7559 (ptmm) cc_final: 0.7102 (mmtt) REVERT: A 555 ARG cc_start: 0.7249 (mtm-85) cc_final: 0.7047 (mtm-85) REVERT: A 608 ASP cc_start: 0.7677 (t0) cc_final: 0.7272 (t0) REVERT: A 668 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7775 (tmm) REVERT: A 718 LYS cc_start: 0.7695 (tptt) cc_final: 0.7423 (tptp) REVERT: A 722 ASN cc_start: 0.7673 (t0) cc_final: 0.7223 (t0) REVERT: A 857 GLU cc_start: 0.7465 (mp0) cc_final: 0.6870 (tp30) REVERT: A 911 ASN cc_start: 0.7859 (p0) cc_final: 0.7625 (p0) REVERT: B 157 GLN cc_start: 0.8311 (mt0) cc_final: 0.7777 (tt0) REVERT: B 164 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.8072 (m) REVERT: B 174 MET cc_start: 0.7943 (mmt) cc_final: 0.7385 (tpt) REVERT: C 21 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7755 (tpp-160) REVERT: D 50 ASP cc_start: 0.6949 (OUTLIER) cc_final: 0.6075 (m-30) REVERT: D 62 MET cc_start: 0.7245 (tpp) cc_final: 0.6944 (ttp) REVERT: D 78 ASP cc_start: 0.7304 (t0) cc_final: 0.7062 (t0) REVERT: D 164 SER cc_start: 0.7284 (m) cc_final: 0.6951 (t) outliers start: 46 outliers final: 26 residues processed: 169 average time/residue: 0.1082 time to fit residues: 26.9633 Evaluate side-chains 161 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 28 optimal weight: 0.0970 chunk 57 optimal weight: 0.1980 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN A 497 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.150448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114131 restraints weight = 14686.740| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.59 r_work: 0.3192 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.8147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12986 Z= 0.109 Angle : 0.565 8.527 17973 Z= 0.266 Chirality : 0.044 0.318 2101 Planarity : 0.003 0.043 2007 Dihedral : 9.981 167.290 2398 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.59 % Allowed : 17.99 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1365 helix: 1.03 (0.20), residues: 702 sheet: -0.80 (0.45), residues: 124 loop : -1.11 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 750 TYR 0.013 0.001 TYR A 788 PHE 0.012 0.001 PHE A 741 TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (12978) covalent geometry : angle 0.56344 / 0.27 (17967) hydrogen bonds : bond 0.03059 / 2.01 ( 631) hydrogen bonds : angle 3.73176 / 2.61 ( 1707) metal coordination : bond 0.00397 / 0.20 ( 8) metal coordination : angle 2.15289 / 1.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.459 Fit side-chains REVERT: A 40 ASP cc_start: 0.8227 (m-30) cc_final: 0.7764 (p0) REVERT: A 235 ASP cc_start: 0.7793 (m-30) cc_final: 0.7103 (p0) REVERT: A 268 TRP cc_start: 0.8131 (OUTLIER) cc_final: 0.5249 (m-90) REVERT: A 277 GLU cc_start: 0.7700 (tp30) cc_final: 0.7225 (mp0) REVERT: A 332 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7640 (ttmm) REVERT: A 441 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8534 (t80) REVERT: A 551 LYS cc_start: 0.7442 (ptmm) cc_final: 0.7048 (mmtt) REVERT: A 608 ASP cc_start: 0.7682 (t0) cc_final: 0.7329 (t0) REVERT: A 722 ASN cc_start: 0.7704 (t0) cc_final: 0.7179 (m-40) REVERT: A 815 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8103 (mt0) REVERT: A 857 GLU cc_start: 0.7552 (mp0) cc_final: 0.6673 (tp30) REVERT: A 911 ASN cc_start: 0.7845 (p0) cc_final: 0.7598 (p0) REVERT: B 157 GLN cc_start: 0.8331 (mt0) cc_final: 0.7846 (tt0) REVERT: B 174 MET cc_start: 0.7971 (mmt) cc_final: 0.7452 (tpt) REVERT: C 21 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7751 (tpp-160) REVERT: C 43 LYS cc_start: 0.8722 (mmtm) cc_final: 0.8336 (mmmt) REVERT: D 50 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6071 (m-30) REVERT: D 62 MET cc_start: 0.7338 (tpp) cc_final: 0.7027 (ttp) REVERT: D 78 ASP cc_start: 0.7300 (t0) cc_final: 0.7033 (t0) REVERT: D 97 LYS cc_start: 0.8382 (tttm) cc_final: 0.7981 (ttmm) REVERT: D 164 SER cc_start: 0.7465 (m) cc_final: 0.6885 (t) REVERT: D 179 ASN cc_start: 0.4686 (m110) cc_final: 0.4396 (m-40) outliers start: 31 outliers final: 15 residues processed: 160 average time/residue: 0.1114 time to fit residues: 26.5679 Evaluate side-chains 151 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 172 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 94 optimal weight: 0.0050 chunk 136 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.148385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111854 restraints weight = 14725.115| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.58 r_work: 0.3164 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.8367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12986 Z= 0.143 Angle : 0.590 8.522 17973 Z= 0.280 Chirality : 0.045 0.320 2101 Planarity : 0.003 0.044 2007 Dihedral : 9.923 162.275 2398 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.85 % Allowed : 17.74 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.23), residues: 1365 helix: 1.04 (0.20), residues: 703 sheet: -0.81 (0.44), residues: 131 loop : -1.03 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 553 TYR 0.012 0.001 TYR A 788 PHE 0.014 0.001 PHE A 741 TRP 0.011 0.001 TRP A 509 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (12978) covalent geometry : angle 0.58871 / 0.28 (17967) hydrogen bonds : bond 0.03234 / 2.14 ( 631) hydrogen bonds : angle 3.73828 / 2.61 ( 1707) metal coordination : bond 0.00900 / 0.47 ( 8) metal coordination : angle 2.23703 / 1.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.429 Fit side-chains REVERT: A 40 ASP cc_start: 0.8272 (m-30) cc_final: 0.7842 (p0) REVERT: A 235 ASP cc_start: 0.7806 (m-30) cc_final: 0.7155 (p0) REVERT: A 268 TRP cc_start: 0.8166 (OUTLIER) cc_final: 0.5287 (m-90) REVERT: A 277 GLU cc_start: 0.7750 (tp30) cc_final: 0.7262 (mp0) REVERT: A 332 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7665 (ttmm) REVERT: A 404 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8283 (p0) REVERT: A 431 GLU cc_start: 0.7321 (tp30) cc_final: 0.6439 (tt0) REVERT: A 551 LYS cc_start: 0.7634 (ptmm) cc_final: 0.7177 (mmtt) REVERT: A 608 ASP cc_start: 0.7698 (t0) cc_final: 0.7309 (t0) REVERT: A 722 ASN cc_start: 0.7698 (t0) cc_final: 0.7173 (m-40) REVERT: A 815 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8126 (mt0) REVERT: A 857 GLU cc_start: 0.7642 (mp0) cc_final: 0.6818 (tp30) REVERT: A 911 ASN cc_start: 0.7810 (p0) cc_final: 0.7560 (p0) REVERT: B 157 GLN cc_start: 0.8342 (mt0) cc_final: 0.7859 (tt0) REVERT: B 174 MET cc_start: 0.8016 (mmt) cc_final: 0.7538 (tpt) REVERT: C 43 LYS cc_start: 0.8738 (mmtm) cc_final: 0.8355 (mmmt) REVERT: D 50 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6142 (m-30) REVERT: D 62 MET cc_start: 0.7403 (tpp) cc_final: 0.7104 (ttp) REVERT: D 78 ASP cc_start: 0.7587 (t0) cc_final: 0.7370 (t0) REVERT: D 97 LYS cc_start: 0.8390 (tttm) cc_final: 0.8049 (ttmm) REVERT: D 164 SER cc_start: 0.7501 (m) cc_final: 0.7024 (t) REVERT: D 179 ASN cc_start: 0.5157 (m110) cc_final: 0.4739 (m-40) outliers start: 34 outliers final: 23 residues processed: 160 average time/residue: 0.1056 time to fit residues: 25.2662 Evaluate side-chains 158 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 132 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 108 optimal weight: 0.0170 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN A 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.146461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.109802 restraints weight = 14656.057| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.63 r_work: 0.3181 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.8775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12986 Z= 0.168 Angle : 0.609 8.520 17973 Z= 0.290 Chirality : 0.045 0.322 2101 Planarity : 0.003 0.046 2007 Dihedral : 9.887 152.757 2398 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.01 % Allowed : 17.82 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.23), residues: 1365 helix: 1.00 (0.20), residues: 704 sheet: -0.84 (0.44), residues: 131 loop : -1.05 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 553 TYR 0.013 0.001 TYR A 80 PHE 0.014 0.001 PHE A 741 TRP 0.011 0.001 TRP A 509 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (12978) covalent geometry : angle 0.60809 / 0.29 (17967) hydrogen bonds : bond 0.03429 / 2.29 ( 631) hydrogen bonds : angle 3.80516 / 2.66 ( 1707) metal coordination : bond 0.01022 / 0.54 ( 8) metal coordination : angle 2.23262 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.466 Fit side-chains REVERT: A 40 ASP cc_start: 0.8306 (m-30) cc_final: 0.7893 (p0) REVERT: A 235 ASP cc_start: 0.7839 (m-30) cc_final: 0.7094 (p0) REVERT: A 268 TRP cc_start: 0.8177 (OUTLIER) cc_final: 0.5355 (m-90) REVERT: A 277 GLU cc_start: 0.7769 (tp30) cc_final: 0.7285 (mp0) REVERT: A 332 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7720 (ttmm) REVERT: A 431 GLU cc_start: 0.7429 (tp30) cc_final: 0.6493 (tt0) REVERT: A 551 LYS cc_start: 0.7708 (ptmm) cc_final: 0.7424 (mmtt) REVERT: A 553 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7500 (mtm-85) REVERT: A 608 ASP cc_start: 0.7746 (t0) cc_final: 0.7291 (t0) REVERT: A 722 ASN cc_start: 0.7604 (t0) cc_final: 0.7055 (m-40) REVERT: A 815 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: A 857 GLU cc_start: 0.7851 (mp0) cc_final: 0.6861 (tp30) REVERT: A 911 ASN cc_start: 0.7807 (p0) cc_final: 0.7566 (p0) REVERT: B 67 MET cc_start: 0.5142 (tpp) cc_final: 0.4139 (tmm) REVERT: B 112 ASP cc_start: 0.7497 (m-30) cc_final: 0.7231 (m-30) REVERT: B 157 GLN cc_start: 0.8310 (mt0) cc_final: 0.7823 (tt0) REVERT: B 174 MET cc_start: 0.8043 (mmt) cc_final: 0.7579 (tpt) REVERT: C 43 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8517 (mmtm) REVERT: D 50 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6436 (m-30) REVERT: D 62 MET cc_start: 0.7355 (tpp) cc_final: 0.7022 (ttp) REVERT: D 97 LYS cc_start: 0.8242 (tttm) cc_final: 0.7919 (ttmm) REVERT: D 164 SER cc_start: 0.7421 (m) cc_final: 0.6980 (t) outliers start: 36 outliers final: 25 residues processed: 155 average time/residue: 0.1154 time to fit residues: 26.6054 Evaluate side-chains 153 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 11 optimal weight: 0.0060 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 HIS D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111748 restraints weight = 14744.785| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.58 r_work: 0.3174 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.8868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12986 Z= 0.124 Angle : 0.585 8.507 17973 Z= 0.277 Chirality : 0.045 0.318 2101 Planarity : 0.003 0.043 2007 Dihedral : 9.822 148.697 2398 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.34 % Allowed : 18.49 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1365 helix: 1.13 (0.20), residues: 703 sheet: -0.79 (0.43), residues: 129 loop : -0.98 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 553 TYR 0.013 0.001 TYR A 788 PHE 0.013 0.001 PHE A 741 TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (12978) covalent geometry : angle 0.58382 / 0.28 (17967) hydrogen bonds : bond 0.03182 / 2.12 ( 631) hydrogen bonds : angle 3.73363 / 2.61 ( 1707) metal coordination : bond 0.00800 / 0.42 ( 8) metal coordination : angle 2.15280 / 1.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.467 Fit side-chains REVERT: A 40 ASP cc_start: 0.8306 (m-30) cc_final: 0.7912 (p0) REVERT: A 235 ASP cc_start: 0.7866 (m-30) cc_final: 0.7215 (p0) REVERT: A 268 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.5458 (m-90) REVERT: A 277 GLU cc_start: 0.7799 (tp30) cc_final: 0.7343 (mp0) REVERT: A 332 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7842 (ttmm) REVERT: A 431 GLU cc_start: 0.7415 (tp30) cc_final: 0.6479 (tt0) REVERT: A 551 LYS cc_start: 0.7690 (ptmm) cc_final: 0.7454 (mmtt) REVERT: A 553 ARG cc_start: 0.8113 (ttm110) cc_final: 0.7721 (mtm-85) REVERT: A 608 ASP cc_start: 0.7686 (t0) cc_final: 0.7272 (t0) REVERT: A 722 ASN cc_start: 0.7714 (t0) cc_final: 0.7180 (m-40) REVERT: A 815 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8150 (mt0) REVERT: A 857 GLU cc_start: 0.7829 (mp0) cc_final: 0.6799 (tp30) REVERT: A 883 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7488 (tp) REVERT: A 911 ASN cc_start: 0.7804 (p0) cc_final: 0.7581 (p0) REVERT: B 67 MET cc_start: 0.5224 (tpp) cc_final: 0.4198 (tmm) REVERT: B 112 ASP cc_start: 0.7524 (m-30) cc_final: 0.7282 (m-30) REVERT: B 157 GLN cc_start: 0.8499 (mt0) cc_final: 0.7897 (tt0) REVERT: B 174 MET cc_start: 0.8135 (mmt) cc_final: 0.7715 (tpt) REVERT: C 43 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8349 (mmtt) REVERT: C 62 MET cc_start: 0.7359 (mtm) cc_final: 0.7098 (mtm) REVERT: D 50 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6606 (m-30) REVERT: D 62 MET cc_start: 0.7355 (tpp) cc_final: 0.7057 (ttp) REVERT: D 70 MET cc_start: 0.7642 (ttm) cc_final: 0.7388 (ttm) REVERT: D 97 LYS cc_start: 0.8255 (tttm) cc_final: 0.7903 (ttmm) REVERT: D 164 SER cc_start: 0.7474 (m) cc_final: 0.7047 (t) outliers start: 28 outliers final: 17 residues processed: 147 average time/residue: 0.1054 time to fit residues: 23.3538 Evaluate side-chains 140 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 84 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 134 optimal weight: 0.3980 chunk 128 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN A 613 HIS D 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.148602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.111711 restraints weight = 14756.794| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.65 r_work: 0.3097 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.9022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12986 Z= 0.125 Angle : 0.582 8.488 17973 Z= 0.275 Chirality : 0.044 0.317 2101 Planarity : 0.003 0.043 2007 Dihedral : 9.703 140.686 2397 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.43 % Allowed : 18.74 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1365 helix: 1.18 (0.20), residues: 702 sheet: -0.74 (0.43), residues: 131 loop : -0.91 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 553 TYR 0.013 0.001 TYR A 788 PHE 0.014 0.001 PHE A 741 TRP 0.010 0.001 TRP A 509 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (12978) covalent geometry : angle 0.58101 / 0.27 (17967) hydrogen bonds : bond 0.03151 / 2.10 ( 631) hydrogen bonds : angle 3.69146 / 2.58 ( 1707) metal coordination : bond 0.00776 / 0.41 ( 8) metal coordination : angle 2.09324 / 1.03 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.455 Fit side-chains REVERT: A 40 ASP cc_start: 0.8327 (m-30) cc_final: 0.7894 (p0) REVERT: A 235 ASP cc_start: 0.7818 (m-30) cc_final: 0.7132 (p0) REVERT: A 268 TRP cc_start: 0.8139 (OUTLIER) cc_final: 0.5415 (m-90) REVERT: A 277 GLU cc_start: 0.7782 (tp30) cc_final: 0.7220 (mp0) REVERT: A 332 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7782 (ttmm) REVERT: A 408 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: A 415 PHE cc_start: 0.8208 (t80) cc_final: 0.7991 (t80) REVERT: A 431 GLU cc_start: 0.7419 (tp30) cc_final: 0.6480 (tt0) REVERT: A 522 GLU cc_start: 0.7782 (tt0) cc_final: 0.7263 (mp0) REVERT: A 553 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7881 (mtm-85) REVERT: A 608 ASP cc_start: 0.7680 (t0) cc_final: 0.7197 (t0) REVERT: A 722 ASN cc_start: 0.7622 (t0) cc_final: 0.7100 (m-40) REVERT: A 815 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8120 (mt0) REVERT: A 857 GLU cc_start: 0.7880 (mp0) cc_final: 0.6769 (tp30) REVERT: A 883 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7441 (tp) REVERT: A 911 ASN cc_start: 0.7737 (p0) cc_final: 0.7504 (p0) REVERT: B 67 MET cc_start: 0.5139 (tpp) cc_final: 0.4169 (tmm) REVERT: B 112 ASP cc_start: 0.7562 (m-30) cc_final: 0.7348 (m-30) REVERT: B 157 GLN cc_start: 0.8482 (mt0) cc_final: 0.7854 (tt0) REVERT: B 174 MET cc_start: 0.8101 (mmt) cc_final: 0.7696 (tpt) REVERT: C 43 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8317 (mmtt) REVERT: C 62 MET cc_start: 0.7383 (mtm) cc_final: 0.7160 (mtm) REVERT: D 50 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6526 (m-30) REVERT: D 62 MET cc_start: 0.7319 (tpp) cc_final: 0.7106 (ttp) REVERT: D 70 MET cc_start: 0.7730 (ttm) cc_final: 0.7518 (ttm) REVERT: D 97 LYS cc_start: 0.8215 (tttm) cc_final: 0.7844 (ttmm) REVERT: D 164 SER cc_start: 0.7414 (m) cc_final: 0.7006 (t) outliers start: 29 outliers final: 21 residues processed: 146 average time/residue: 0.1069 time to fit residues: 23.5808 Evaluate side-chains 147 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 126 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 HIS D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.148400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111538 restraints weight = 14762.303| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.65 r_work: 0.3206 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.9008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.228 12986 Z= 0.202 Angle : 0.819 59.200 17973 Z= 0.460 Chirality : 0.047 0.772 2101 Planarity : 0.004 0.043 2007 Dihedral : 9.711 140.664 2397 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.68 % Allowed : 18.41 % Favored : 78.91 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1365 helix: 1.18 (0.20), residues: 702 sheet: -0.74 (0.43), residues: 131 loop : -0.91 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 553 TYR 0.013 0.001 TYR A 788 PHE 0.014 0.001 PHE A 741 TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 (12978) covalent geometry : angle 0.81846 / 0.46 (17967) hydrogen bonds : bond 0.03154 / 2.11 ( 631) hydrogen bonds : angle 3.69117 / 2.58 ( 1707) metal coordination : bond 0.00772 / 0.40 ( 8) metal coordination : angle 2.08850 / 1.03 ( 6) =============================================================================== Job complete usr+sys time: 3305.34 seconds wall clock time: 57 minutes 25.39 seconds (3445.39 seconds total)