Starting phenix.real_space_refine on Thu Mar 5 19:09:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n9b_24255/03_2026/7n9b_24255.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n9b_24255/03_2026/7n9b_24255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n9b_24255/03_2026/7n9b_24255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n9b_24255/03_2026/7n9b_24255.map" model { file = "/net/cci-nas-00/data/ceres_data/7n9b_24255/03_2026/7n9b_24255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n9b_24255/03_2026/7n9b_24255.cif" } resolution = 3.8 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 15696 2.51 5 N 4112 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24575 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7631 Classifications: {'peptide': 989} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 53, 'TRANS': 935} Chain breaks: 8 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 3, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 7560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7560 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'ASN:plan1': 4, 'GLU:plan': 8, 'GLN:plan1': 3, 'ARG:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7618 Classifications: {'peptide': 988} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 52, 'TRANS': 935} Chain breaks: 9 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 885 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "F" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 881 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.71, per 1000 atoms: 0.19 Number of scatterers: 24575 At special positions: 0 Unit cell: (136.95, 122.84, 195.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 4661 8.00 N 4112 7.00 C 15696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 428 " - pdb=" SG CYS A 453 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 617 " distance=2.05 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 580 " distance=2.02 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 682 " distance=2.01 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 741 " distance=2.02 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 841 " distance=2.01 Simple disulfide: pdb=" SG CYS A1124 " - pdb=" SG CYS A1135 " distance=2.00 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 258 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 453 " distance=2.04 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 617 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 580 " distance=2.04 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 709 " - pdb=" SG CYS B 741 " distance=2.03 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 841 " distance=2.03 Simple disulfide: pdb=" SG CYS B1124 " - pdb=" SG CYS B1135 " distance=2.00 Simple disulfide: pdb=" SG CYS B1174 " - pdb=" SG CYS B1218 " distance=2.02 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 393 " distance=2.04 Simple disulfide: pdb=" SG CYS C 428 " - pdb=" SG CYS C 453 " distance=2.02 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 524 " distance=2.03 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 617 " distance=2.02 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 580 " distance=2.00 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 682 " distance=2.03 Simple disulfide: pdb=" SG CYS C 709 " - pdb=" SG CYS C 741 " distance=2.03 Simple disulfide: pdb=" SG CYS C 754 " - pdb=" SG CYS C 763 " distance=2.03 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 841 " distance=2.02 Simple disulfide: pdb=" SG CYS C1124 " - pdb=" SG CYS C1135 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 94 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 94 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5960 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 56 sheets defined 24.7% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 429 through 435 removed outlier: 4.240A pdb=" N VAL A 433 " --> pdb=" O PRO A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 456 through 463 removed outlier: 3.792A pdb=" N LEU A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.752A pdb=" N LEU A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASN A 480 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 4.626A pdb=" N ARG A 500 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 514 Processing helix chain 'A' and resid 829 through 835 Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.740A pdb=" N LEU A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 875 removed outlier: 3.500A pdb=" N LEU A 855 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 867 " --> pdb=" O ALA A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 917 Processing helix chain 'A' and resid 958 through 976 Processing helix chain 'A' and resid 977 through 980 removed outlier: 4.103A pdb=" N PHE A 980 " --> pdb=" O GLY A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 980' Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.554A pdb=" N ILE A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1011 removed outlier: 3.531A pdb=" N TYR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1033 removed outlier: 3.793A pdb=" N GLN A1027 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A1028 " --> pdb=" O GLY A1024 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR A1033 " --> pdb=" O SER A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1057 Processing helix chain 'A' and resid 1058 through 1060 No H-bonds generated for 'chain 'A' and resid 1058 through 1060' Processing helix chain 'A' and resid 1068 through 1076 removed outlier: 3.746A pdb=" N LEU A1076 " --> pdb=" O ILE A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1124 removed outlier: 4.718A pdb=" N VAL A1083 " --> pdb=" O PRO A1079 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A1084 " --> pdb=" O GLU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1239 Processing helix chain 'B' and resid 386 through 396 Processing helix chain 'B' and resid 429 through 435 removed outlier: 4.000A pdb=" N VAL B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.892A pdb=" N ILE B 502 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 514 Processing helix chain 'B' and resid 530 through 535 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 829 through 836 Processing helix chain 'B' and resid 838 through 846 removed outlier: 3.557A pdb=" N LEU B 846 " --> pdb=" O SER B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 849 No H-bonds generated for 'chain 'B' and resid 847 through 849' Processing helix chain 'B' and resid 852 through 875 removed outlier: 3.587A pdb=" N ASP B 867 " --> pdb=" O ALA B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 918 Processing helix chain 'B' and resid 958 through 977 Processing helix chain 'B' and resid 978 through 981 Processing helix chain 'B' and resid 989 through 1002 Processing helix chain 'B' and resid 1004 through 1011 removed outlier: 4.348A pdb=" N LEU B1008 " --> pdb=" O THR B1004 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B1009 " --> pdb=" O GLN B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1033 Processing helix chain 'B' and resid 1037 through 1057 Processing helix chain 'B' and resid 1058 through 1060 No H-bonds generated for 'chain 'B' and resid 1058 through 1060' Processing helix chain 'B' and resid 1068 through 1074 Processing helix chain 'B' and resid 1077 through 1126 removed outlier: 4.415A pdb=" N VAL B1083 " --> pdb=" O PRO B1079 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN B1084 " --> pdb=" O GLU B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1232 through 1239 removed outlier: 4.094A pdb=" N GLU B1236 " --> pdb=" O PRO B1232 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B1239 " --> pdb=" O PRO B1235 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 395 Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 441 through 445 removed outlier: 3.755A pdb=" N TRP C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 463 removed outlier: 4.059A pdb=" N LEU C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 497 through 499 No H-bonds generated for 'chain 'C' and resid 497 through 499' Processing helix chain 'C' and resid 508 through 514 Processing helix chain 'C' and resid 594 through 597 Processing helix chain 'C' and resid 829 through 835 Processing helix chain 'C' and resid 838 through 846 removed outlier: 3.643A pdb=" N LEU C 844 " --> pdb=" O GLU C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 849 No H-bonds generated for 'chain 'C' and resid 847 through 849' Processing helix chain 'C' and resid 850 through 875 removed outlier: 3.595A pdb=" N LEU C 855 " --> pdb=" O PHE C 851 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C 856 " --> pdb=" O CYS C 852 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C 867 " --> pdb=" O ALA C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 918 removed outlier: 3.572A pdb=" N LEU C 913 " --> pdb=" O PRO C 909 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 918 " --> pdb=" O LEU C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 976 Processing helix chain 'C' and resid 977 through 980 removed outlier: 3.669A pdb=" N PHE C 980 " --> pdb=" O GLY C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 977 through 980' Processing helix chain 'C' and resid 989 through 1002 Processing helix chain 'C' and resid 1005 through 1011 Processing helix chain 'C' and resid 1011 through 1033 removed outlier: 3.769A pdb=" N GLN C1027 " --> pdb=" O ILE C1023 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP C1028 " --> pdb=" O GLY C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1057 Processing helix chain 'C' and resid 1058 through 1060 No H-bonds generated for 'chain 'C' and resid 1058 through 1060' Processing helix chain 'C' and resid 1068 through 1075 Processing helix chain 'C' and resid 1077 through 1125 removed outlier: 4.451A pdb=" N VAL C1083 " --> pdb=" O PRO C1079 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN C1084 " --> pdb=" O GLU C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1232 through 1239 removed outlier: 4.043A pdb=" N GLU C1236 " --> pdb=" O PRO C1232 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'F' and resid 85 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 123 removed outlier: 3.622A pdb=" N THR A 121 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 154 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASN A 153 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR A 361 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 356 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR A 358 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 182 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 280 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 319 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER A 297 " --> pdb=" O PRO A 317 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL A 128 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 147 removed outlier: 3.742A pdb=" N ASP A 379 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 177 removed outlier: 4.110A pdb=" N GLY A 195 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 411 removed outlier: 5.418A pdb=" N ILE A 404 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 691 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLN A 406 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 689 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 408 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 686 " --> pdb=" O GLN A 705 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 741 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 450 removed outlier: 3.529A pdb=" N TYR A 488 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 448 through 450 removed outlier: 3.529A pdb=" N TYR A 488 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA8, first strand: chain 'A' and resid 544 through 546 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AB1, first strand: chain 'A' and resid 630 through 635 removed outlier: 3.517A pdb=" N GLY A 642 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 635 " --> pdb=" O LEU A 638 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 745 through 747 removed outlier: 5.977A pdb=" N GLU A 746 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N THR A 788 " --> pdb=" O GLU A 746 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 783 " --> pdb=" O GLN A 767 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 762 " --> pdb=" O ILE A 758 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 793 through 796 removed outlier: 6.784A pdb=" N ALA A 793 " --> pdb=" O ILE C 880 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LYS C 882 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN A 795 " --> pdb=" O LYS C 882 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 803 through 806 Processing sheet with id=AB5, first strand: chain 'A' and resid 813 through 820 removed outlier: 6.009A pdb=" N TYR A1159 " --> pdb=" O HIS A1140 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N HIS A1140 " --> pdb=" O TYR A1159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 826 through 828 Processing sheet with id=AB7, first strand: chain 'A' and resid 879 through 882 removed outlier: 3.701A pdb=" N LYS A 882 " --> pdb=" O ASN B 795 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1212 through 1213 Processing sheet with id=AB9, first strand: chain 'A' and resid 1186 through 1188 Processing sheet with id=AC1, first strand: chain 'B' and resid 120 through 123 removed outlier: 3.858A pdb=" N VAL B 359 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 186 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG B 282 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B 287 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE B 295 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 147 removed outlier: 3.531A pdb=" N LEU B 368 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP B 379 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.625A pdb=" N LEU B 176 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 330 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 210 through 213 Processing sheet with id=AC5, first strand: chain 'B' and resid 403 through 409 removed outlier: 3.533A pdb=" N THR B 691 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 687 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B 741 " --> pdb=" O TYR B 704 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY B 740 " --> pdb=" O THR B 737 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 416 through 418 removed outlier: 3.894A pdb=" N GLU B 416 " --> pdb=" O CYS B 630 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 446 through 450 removed outlier: 4.077A pdb=" N ASN B 446 " --> pdb=" O SER B 491 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 491 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 608 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 527 " --> pdb=" O THR B 468 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 468 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 544 through 546 Processing sheet with id=AC9, first strand: chain 'B' and resid 746 through 747 removed outlier: 6.712A pdb=" N ILE B 762 " --> pdb=" O ILE B 758 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 803 through 807 Processing sheet with id=AD2, first strand: chain 'B' and resid 810 through 814 Processing sheet with id=AD3, first strand: chain 'B' and resid 810 through 814 removed outlier: 5.950A pdb=" N TYR B1159 " --> pdb=" O HIS B1140 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N HIS B1140 " --> pdb=" O TYR B1159 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 826 through 828 Processing sheet with id=AD5, first strand: chain 'B' and resid 1212 through 1213 Processing sheet with id=AD6, first strand: chain 'B' and resid 1186 through 1188 Processing sheet with id=AD7, first strand: chain 'C' and resid 120 through 122 removed outlier: 7.909A pdb=" N ASN C 153 " --> pdb=" O TYR C 361 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR C 361 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 188 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN C 280 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE C 293 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP C 320 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 295 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL C 128 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 147 removed outlier: 3.560A pdb=" N ASP C 145 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 368 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP C 379 " --> pdb=" O LYS C 370 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.599A pdb=" N ARG C 329 " --> pdb=" O GLY C 199 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 211 through 213 Processing sheet with id=AE2, first strand: chain 'C' and resid 403 through 406 removed outlier: 3.752A pdb=" N GLY C 740 " --> pdb=" O THR C 737 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 446 through 450 removed outlier: 3.527A pdb=" N ASN C 446 " --> pdb=" O SER C 491 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN C 486 " --> pdb=" O GLU C 608 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 488 " --> pdb=" O SER C 606 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 490 " --> pdb=" O VAL C 604 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 544 through 546 Processing sheet with id=AE5, first strand: chain 'C' and resid 565 through 566 removed outlier: 3.652A pdb=" N TYR C 581 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 634 through 635 removed outlier: 3.540A pdb=" N PHE C 635 " --> pdb=" O LEU C 638 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 643 through 646 Processing sheet with id=AE8, first strand: chain 'C' and resid 745 through 747 removed outlier: 6.110A pdb=" N GLU C 746 " --> pdb=" O ALA C 786 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR C 788 " --> pdb=" O GLU C 746 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE C 762 " --> pdb=" O ILE C 758 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 803 through 806 Processing sheet with id=AF1, first strand: chain 'C' and resid 810 through 820 removed outlier: 3.557A pdb=" N MET C1142 " --> pdb=" O VAL C1157 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR C1159 " --> pdb=" O HIS C1140 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS C1140 " --> pdb=" O TYR C1159 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 825 through 828 removed outlier: 4.468A pdb=" N LYS C 825 " --> pdb=" O LEU C 953 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1212 through 1214 Processing sheet with id=AF4, first strand: chain 'C' and resid 1186 through 1189 Processing sheet with id=AF5, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.665A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR D 67 " --> pdb=" O GLN D 80 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.800A pdb=" N VAL D 12 " --> pdb=" O SER D 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.072A pdb=" N ASN D 57 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 48 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE D 45 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG D 36 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 32 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 31 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 91 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.072A pdb=" N ASN D 57 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 48 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE D 45 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG D 36 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 32 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 31 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 91 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 113 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 4 through 7 removed outlier: 4.350A pdb=" N LEU F 20 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 79 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS F 22 " --> pdb=" O ILE F 77 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.687A pdb=" N ALA F 47 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG F 36 " --> pdb=" O PHE F 45 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE F 45 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA F 48 " --> pdb=" O ASN F 57 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN F 57 " --> pdb=" O ALA F 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 11 through 13 974 hydrogen bonds defined for protein. 2643 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4026 1.27 - 1.41: 6435 1.41 - 1.55: 14530 1.55 - 1.68: 0 1.68 - 1.82: 132 Bond restraints: 25123 Sorted by residual: bond pdb=" CD GLU A 576 " pdb=" OE2 GLU A 576 " ideal model delta sigma weight residual 1.249 1.137 0.112 1.90e-02 2.77e+03 3.45e+01 bond pdb=" C PRO A 820 " pdb=" O PRO A 820 " ideal model delta sigma weight residual 1.233 1.170 0.063 1.16e-02 7.43e+03 2.92e+01 bond pdb=" C PRO B1149 " pdb=" O PRO B1149 " ideal model delta sigma weight residual 1.233 1.172 0.061 1.13e-02 7.83e+03 2.91e+01 bond pdb=" CA SER B1113 " pdb=" CB SER B1113 " ideal model delta sigma weight residual 1.528 1.448 0.081 1.59e-02 3.96e+03 2.57e+01 bond pdb=" CA SER A1129 " pdb=" CB SER A1129 " ideal model delta sigma weight residual 1.531 1.454 0.077 1.52e-02 4.33e+03 2.56e+01 ... (remaining 25118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 34075 4.88 - 9.77: 137 9.77 - 14.65: 2 14.65 - 19.53: 0 19.53 - 24.42: 2 Bond angle restraints: 34216 Sorted by residual: angle pdb=" CE2 TYR C 581 " pdb=" CZ TYR C 581 " pdb=" OH TYR C 581 " ideal model delta sigma weight residual 119.90 95.48 24.42 3.00e+00 1.11e-01 6.63e+01 angle pdb=" N THR A 710 " pdb=" CA THR A 710 " pdb=" C THR A 710 " ideal model delta sigma weight residual 113.38 103.52 9.86 1.23e+00 6.61e-01 6.43e+01 angle pdb=" N THR C 710 " pdb=" CA THR C 710 " pdb=" C THR C 710 " ideal model delta sigma weight residual 113.17 103.82 9.35 1.26e+00 6.30e-01 5.51e+01 angle pdb=" N THR F 101 " pdb=" CA THR F 101 " pdb=" C THR F 101 " ideal model delta sigma weight residual 114.04 105.74 8.30 1.24e+00 6.50e-01 4.48e+01 angle pdb=" CE1 TYR C 581 " pdb=" CZ TYR C 581 " pdb=" OH TYR C 581 " ideal model delta sigma weight residual 119.90 139.88 -19.98 3.00e+00 1.11e-01 4.44e+01 ... (remaining 34211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 13494 17.88 - 35.75: 1149 35.75 - 53.63: 198 53.63 - 71.50: 33 71.50 - 89.38: 34 Dihedral angle restraints: 14908 sinusoidal: 5642 harmonic: 9266 Sorted by residual: dihedral pdb=" CB CYS A1124 " pdb=" SG CYS A1124 " pdb=" SG CYS A1135 " pdb=" CB CYS A1135 " ideal model delta sinusoidal sigma weight residual -86.00 -170.76 84.76 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS C 754 " pdb=" SG CYS C 754 " pdb=" SG CYS C 763 " pdb=" CB CYS C 763 " ideal model delta sinusoidal sigma weight residual -86.00 -9.88 -76.12 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS C1124 " pdb=" SG CYS C1124 " pdb=" SG CYS C1135 " pdb=" CB CYS C1135 " ideal model delta sinusoidal sigma weight residual -86.00 -158.97 72.97 1 1.00e+01 1.00e-02 6.79e+01 ... (remaining 14905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 3187 0.131 - 0.262: 723 0.262 - 0.394: 14 0.394 - 0.525: 1 0.525 - 0.656: 2 Chirality restraints: 3927 Sorted by residual: chirality pdb=" CA CYS C 709 " pdb=" N CYS C 709 " pdb=" C CYS C 709 " pdb=" CB CYS C 709 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" CA CYS A 709 " pdb=" N CYS A 709 " pdb=" C CYS A 709 " pdb=" CB CYS A 709 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 3924 not shown) Planarity restraints: 4433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 581 " -0.057 2.00e-02 2.50e+03 3.98e-02 3.17e+01 pdb=" CG TYR C 581 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR C 581 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR C 581 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR C 581 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR C 581 " 0.054 2.00e-02 2.50e+03 pdb=" CZ TYR C 581 " -0.055 2.00e-02 2.50e+03 pdb=" OH TYR C 581 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 45 " -0.014 2.00e-02 2.50e+03 3.16e-02 1.75e+01 pdb=" CG PHE D 45 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE D 45 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 PHE D 45 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE D 45 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 PHE D 45 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 45 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 85 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C LYS D 85 " -0.065 2.00e-02 2.50e+03 pdb=" O LYS D 85 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO D 86 " 0.022 2.00e-02 2.50e+03 ... (remaining 4430 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 470 2.64 - 3.20: 23060 3.20 - 3.77: 36222 3.77 - 4.33: 50626 4.33 - 4.90: 84267 Nonbonded interactions: 194645 Sorted by model distance: nonbonded pdb=" OH TYR A 581 " pdb=" O THR D 101 " model vdw 2.070 3.040 nonbonded pdb=" O THR A 485 " pdb=" OG1 THR A 615 " model vdw 2.203 3.040 nonbonded pdb=" O ASP A 386 " pdb=" OG SER A 389 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR C 129 " pdb=" O LEU C 146 " model vdw 2.227 3.040 nonbonded pdb=" OE1 GLN D 1 " pdb=" OH TYR D 106 " model vdw 2.254 3.040 ... (remaining 194640 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 'A' and (resid 119 through 144 or (resid 145 and (name N or name CA or na \ me C or name O or name CB )) or resid 146 through 158 or resid 174 through 187 o \ r (resid 188 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 89 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 200 or (resid 201 through 205 and (name N or name CA \ or name C or name O or name CB )) or resid 208 through 216 or (resid 217 and (na \ me N or name CA or name C or name O or name CB )) or resid 218 through 223 or (r \ esid 224 and (name N or name CA or name C or name O or name CB )) or resid 225 o \ r (resid 226 through 230 and (name N or name CA or name C or name O or name CB ) \ ) or resid 231 through 232 or resid 259 through 263 or (resid 264 and (name N or \ name CA or name C or name O or name CB )) or resid 278 through 288 or resid 292 \ through 303 or (resid 307 and (name N or name CA or name C or name O or name CB \ )) or resid 308 through 309 or (resid 310 and (name N or name CA or name C or n \ ame O or name CB )) or resid 311 through 315 or (resid 316 and (name N or name C \ A or name C or name O or name CB )) or resid 317 through 330 or (resid 331 and ( \ name N or name CA or name C or name O or name CB )) or resid 332 through 400 or \ (resid 401 and (name N or name CA or name C or name O or name CB )) or resid 402 \ through 424 or (resid 425 and (name N or name CA or name C or name O or name CB \ )) or resid 426 through 477 or (resid 478 and (name N or name CA or name C or n \ ame O or name CB )) or resid 479 through 499 or (resid 500 and (name N or name C \ A or name C or name O or name CB )) or resid 501 through 515 or (resid 516 and ( \ name N or name CA or name C or name O or name CB )) or resid 517 through 520 or \ (resid 521 and (name N or name CA or name C or name O or name CB )) or resid 522 \ through 549 or (resid 550 and (name N or name CA or name C or name O or name CB \ )) or resid 551 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 581 or (resid 582 and (name N or name C \ A or name C or name O or name CB )) or resid 583 through 620 or (resid 621 and ( \ name N or name CA or name C or name O or name CB )) or resid 622 through 645 or \ (resid 646 and (name N or name CA or name C or name O or name CB )) or resid 647 \ through 649 or (resid 650 and (name N or name CA or name C or name O or name CB \ )) or resid 651 or (resid 652 and (name N or name CA or name C or name O or nam \ e CB )) or resid 653 through 669 or (resid 670 and (name N or name CA or name C \ or name O or name CB )) or resid 671 through 885 or (resid 886 and (name N or na \ me CA or name C or name O or name CB )) or resid 887 or (resid 888 and (name N o \ r name CA or name C or name O or name CB )) or resid 889 through 903 or resid 90 \ 5 through 979 or (resid 980 and (name N or name CA or name C or name O or name C \ B )) or resid 981 through 1239)) selection = (chain 'B' and (resid 119 through 158 or resid 174 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 205 o \ r resid 208 through 220 or (resid 221 and (name N or name CA or name C or name O \ or name CB )) or resid 222 through 226 or (resid 227 through 230 and (name N or \ name CA or name C or name O or name CB )) or resid 231 through 232 or resid 259 \ through 279 or (resid 280 and (name N or name CA or name C or name O or name CB \ )) or resid 281 or (resid 282 and (name N or name CA or name C or name O or nam \ e CB )) or resid 283 through 287 or (resid 288 and (name N or name CA or name C \ or name O or name CB )) or resid 292 through 333 or (resid 334 through 356 and ( \ name N or name CA or name C or name O or name CB )) or resid 357 through 372 or \ (resid 373 and (name N or name CA or name C or name O or name CB )) or resid 374 \ through 448 or (resid 449 and (name N or name CA or name C or name O or name CB \ )) or resid 450 through 515 or (resid 516 and (name N or name CA or name C or n \ ame O or name CB )) or resid 517 through 549 or (resid 550 and (name N or name C \ A or name C or name O or name CB )) or resid 551 through 575 or (resid 576 and ( \ name N or name CA or name C or name O or name CB )) or resid 577 through 581 or \ (resid 582 and (name N or name CA or name C or name O or name CB )) or resid 583 \ through 659 or (resid 660 and (name N or name CA or name C or name O or name CB \ )) or resid 661 through 673 or (resid 674 through 675 and (name N or name CA or \ name C or name O or name CB )) or resid 676 through 677 or (resid 678 and (name \ N or name CA or name C or name O or name CB )) or resid 679 through 705 or (res \ id 706 and (name N or name CA or name C or name O or name CB )) or resid 707 thr \ ough 710 or (resid 711 and (name N or name CA or name C or name O or name CB )) \ or resid 712 through 768 or resid 782 through 836 or (resid 837 and (name N or n \ ame CA or name C or name O or name CB )) or resid 838 through 919 or resid 947 t \ hrough 1239)) selection = (chain 'C' and (resid 119 through 144 or (resid 145 and (name N or name CA or na \ me C or name O or name CB )) or resid 146 through 158 or resid 174 through 187 o \ r (resid 188 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 89 through 200 or (resid 201 through 205 and (name N or name CA or name C or nam \ e O or name CB )) or resid 208 through 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 223 or (resid 224 and (na \ me N or name CA or name C or name O or name CB )) or resid 225 or (resid 226 thr \ ough 230 and (name N or name CA or name C or name O or name CB )) or resid 231 t \ hrough 232 or resid 259 through 263 or (resid 264 and (name N or name CA or name \ C or name O or name CB )) or resid 278 through 281 or (resid 282 and (name N or \ name CA or name C or name O or name CB )) or resid 283 through 288 or resid 292 \ through 303 or (resid 307 and (name N or name CA or name C or name O or name CB \ )) or resid 308 through 309 or (resid 310 and (name N or name CA or name C or n \ ame O or name CB )) or resid 311 through 315 or (resid 316 and (name N or name C \ A or name C or name O or name CB )) or resid 317 through 330 or (resid 331 and ( \ name N or name CA or name C or name O or name CB )) or resid 332 through 400 or \ (resid 401 and (name N or name CA or name C or name O or name CB )) or resid 402 \ through 424 or (resid 425 and (name N or name CA or name C or name O or name CB \ )) or resid 426 through 448 or (resid 449 and (name N or name CA or name C or n \ ame O or name CB )) or resid 450 through 477 or (resid 478 and (name N or name C \ A or name C or name O or name CB )) or resid 479 through 499 or (resid 500 and ( \ name N or name CA or name C or name O or name CB )) or resid 501 through 520 or \ (resid 521 and (name N or name CA or name C or name O or name CB )) or resid 522 \ through 620 or (resid 621 and (name N or name CA or name C or name O or name CB \ )) or resid 622 through 645 or (resid 646 and (name N or name CA or name C or n \ ame O or name CB )) or resid 647 through 649 or (resid 650 and (name N or name C \ A or name C or name O or name CB )) or resid 651 or (resid 652 and (name N or na \ me CA or name C or name O or name CB )) or resid 653 through 659 or (resid 660 a \ nd (name N or name CA or name C or name O or name CB )) or resid 661 through 669 \ or (resid 670 and (name N or name CA or name C or name O or name CB )) or resid \ 671 through 885 or (resid 886 and (name N or name CA or name C or name O or nam \ e CB )) or resid 887 or (resid 888 and (name N or name CA or name C or name O or \ name CB )) or resid 889 through 979 or (resid 980 and (name N or name CA or nam \ e C or name O or name CB )) or resid 981 through 1239)) } ncs_group { reference = (chain 'D' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 117)) selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 20.870 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.013 0.112 25154 Z= 0.938 Angle : 1.417 24.418 34278 Z= 0.989 Chirality : 0.101 0.656 3927 Planarity : 0.007 0.047 4433 Dihedral : 13.967 89.378 8855 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.07 % Allowed : 6.15 % Favored : 93.78 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.41 (0.14), residues: 3133 helix: 1.82 (0.19), residues: 654 sheet: -0.19 (0.19), residues: 686 loop : -1.13 (0.13), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG F 31 TYR 0.057 0.004 TYR C 581 PHE 0.059 0.003 PHE D 45 TRP 0.029 0.004 TRP B 978 HIS 0.008 0.002 HIS B1140 Details of bonding type rmsd covalent geometry : bond 0.01344 (25123) covalent geometry : angle 1.41097 (34216) SS BOND : bond 0.01351 ( 31) SS BOND : angle 3.39878 ( 62) hydrogen bonds : bond 0.21670 ( 950) hydrogen bonds : angle 8.72160 ( 2643) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 292 TYR cc_start: 0.6869 (m-10) cc_final: 0.6577 (m-80) REVERT: A 560 ILE cc_start: 0.7766 (pt) cc_final: 0.7431 (mt) REVERT: B 1042 ASP cc_start: 0.8145 (t70) cc_final: 0.7674 (t70) REVERT: C 397 SER cc_start: 0.8799 (p) cc_final: 0.8552 (p) REVERT: F 81 MET cc_start: 0.2146 (mpp) cc_final: 0.1784 (mtm) outliers start: 2 outliers final: 2 residues processed: 300 average time/residue: 0.1493 time to fit residues: 73.2631 Evaluate side-chains 243 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 1132 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 217 ASN A 452 ASN A 540 ASN A 542 ASN A 993 GLN A1234 GLN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 GLN ** C1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108832 restraints weight = 40634.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111028 restraints weight = 25198.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110510 restraints weight = 16868.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110753 restraints weight = 18243.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111069 restraints weight = 15889.016| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25154 Z= 0.143 Angle : 0.637 10.126 34278 Z= 0.340 Chirality : 0.047 0.169 3927 Planarity : 0.005 0.054 4433 Dihedral : 4.913 26.640 3413 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.93 % Allowed : 10.84 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.33 (0.14), residues: 3133 helix: 2.04 (0.20), residues: 654 sheet: -0.27 (0.18), residues: 710 loop : -1.10 (0.13), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 365 TYR 0.022 0.002 TYR C 545 PHE 0.019 0.001 PHE C 657 TRP 0.019 0.001 TRP D 34 HIS 0.007 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00318 (25123) covalent geometry : angle 0.63473 (34216) SS BOND : bond 0.00357 ( 31) SS BOND : angle 1.41694 ( 62) hydrogen bonds : bond 0.05397 ( 950) hydrogen bonds : angle 6.47443 ( 2643) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 290 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 151 PHE cc_start: 0.7642 (m-80) cc_final: 0.7362 (m-80) REVERT: A 188 GLU cc_start: 0.5849 (mm-30) cc_final: 0.5592 (mm-30) REVERT: A 587 TYR cc_start: 0.7055 (m-10) cc_final: 0.6801 (m-10) REVERT: B 157 PHE cc_start: 0.7284 (m-10) cc_final: 0.6910 (m-10) REVERT: B 287 LYS cc_start: 0.8257 (pttt) cc_final: 0.7987 (pttm) REVERT: B 1042 ASP cc_start: 0.7933 (t70) cc_final: 0.7540 (t70) REVERT: C 600 TYR cc_start: 0.8124 (m-80) cc_final: 0.7758 (m-80) REVERT: C 872 GLU cc_start: 0.8041 (tp30) cc_final: 0.7600 (tp30) REVERT: C 1123 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8112 (mt-10) REVERT: D 19 ARG cc_start: 0.6016 (ttp80) cc_final: 0.5811 (mtp180) REVERT: D 81 MET cc_start: 0.4928 (mtt) cc_final: 0.4531 (ptt) REVERT: F 69 SER cc_start: 0.7569 (t) cc_final: 0.7062 (p) REVERT: F 81 MET cc_start: 0.2499 (mpp) cc_final: 0.2038 (mtm) outliers start: 25 outliers final: 14 residues processed: 303 average time/residue: 0.1524 time to fit residues: 75.2976 Evaluate side-chains 259 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 245 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 2 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 142 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 297 optimal weight: 8.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN A1097 GLN A1166 ASN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1156 HIS D 55 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.151753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109487 restraints weight = 40923.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110346 restraints weight = 36200.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109714 restraints weight = 21381.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109253 restraints weight = 19902.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.109506 restraints weight = 17848.404| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25154 Z= 0.213 Angle : 0.622 10.401 34278 Z= 0.330 Chirality : 0.047 0.318 3927 Planarity : 0.005 0.053 4433 Dihedral : 4.893 28.809 3412 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.86 % Allowed : 13.22 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.49 (0.14), residues: 3133 helix: 1.74 (0.20), residues: 651 sheet: -0.30 (0.19), residues: 701 loop : -1.15 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 365 TYR 0.024 0.002 TYR C 545 PHE 0.031 0.002 PHE A 184 TRP 0.015 0.002 TRP D 34 HIS 0.004 0.001 HIS C1150 Details of bonding type rmsd covalent geometry : bond 0.00510 (25123) covalent geometry : angle 0.61818 (34216) SS BOND : bond 0.00445 ( 31) SS BOND : angle 1.73187 ( 62) hydrogen bonds : bond 0.05295 ( 950) hydrogen bonds : angle 6.16896 ( 2643) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 260 time to evaluate : 0.975 Fit side-chains REVERT: A 492 PHE cc_start: 0.8195 (p90) cc_final: 0.7948 (p90) REVERT: B 157 PHE cc_start: 0.7278 (m-10) cc_final: 0.6961 (m-10) REVERT: B 287 LYS cc_start: 0.8380 (pttt) cc_final: 0.8179 (pttt) REVERT: B 742 LEU cc_start: 0.8887 (tp) cc_final: 0.8662 (mp) REVERT: B 1042 ASP cc_start: 0.8039 (t70) cc_final: 0.7638 (t70) REVERT: C 512 ASP cc_start: 0.6243 (m-30) cc_final: 0.6004 (m-30) REVERT: C 872 GLU cc_start: 0.8018 (tp30) cc_final: 0.7591 (tp30) REVERT: C 1073 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8156 (mp) outliers start: 50 outliers final: 33 residues processed: 291 average time/residue: 0.1457 time to fit residues: 70.0193 Evaluate side-chains 273 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 709 CYS Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 1073 LEU Chi-restraints excluded: chain C residue 1109 GLU Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 112 optimal weight: 0.7980 chunk 287 optimal weight: 0.9990 chunk 310 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 295 optimal weight: 30.0000 chunk 223 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1006 ASN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN C 141 HIS ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 ASN C1049 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.153781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117675 restraints weight = 40614.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117417 restraints weight = 66010.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119562 restraints weight = 51816.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119658 restraints weight = 32657.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121972 restraints weight = 26799.090| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25154 Z= 0.126 Angle : 0.561 9.768 34278 Z= 0.294 Chirality : 0.044 0.256 3927 Planarity : 0.004 0.046 4433 Dihedral : 4.651 30.797 3412 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.05 % Allowed : 14.49 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.41 (0.14), residues: 3133 helix: 1.95 (0.21), residues: 648 sheet: -0.38 (0.19), residues: 698 loop : -1.09 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 365 TYR 0.027 0.001 TYR B 587 PHE 0.018 0.001 PHE C 484 TRP 0.014 0.001 TRP D 34 HIS 0.005 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00287 (25123) covalent geometry : angle 0.55810 (34216) SS BOND : bond 0.00285 ( 31) SS BOND : angle 1.39699 ( 62) hydrogen bonds : bond 0.04506 ( 950) hydrogen bonds : angle 5.77680 ( 2643) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 0.908 Fit side-chains REVERT: A 151 PHE cc_start: 0.7405 (m-80) cc_final: 0.7170 (m-80) REVERT: A 501 GLN cc_start: 0.6900 (mm-40) cc_final: 0.6613 (mm-40) REVERT: A 767 GLN cc_start: 0.6255 (tm-30) cc_final: 0.6020 (tm-30) REVERT: B 157 PHE cc_start: 0.7258 (m-10) cc_final: 0.6987 (m-10) REVERT: B 847 GLN cc_start: 0.8345 (tp40) cc_final: 0.8068 (pt0) REVERT: C 872 GLU cc_start: 0.8042 (tp30) cc_final: 0.7617 (tp30) REVERT: C 1073 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8086 (mp) REVERT: C 1133 ASP cc_start: 0.7925 (t0) cc_final: 0.7634 (t0) REVERT: F 69 SER cc_start: 0.7381 (t) cc_final: 0.6925 (p) REVERT: F 81 MET cc_start: 0.2709 (mtm) cc_final: 0.2305 (mtm) REVERT: F 91 VAL cc_start: 0.6083 (OUTLIER) cc_final: 0.5745 (t) outliers start: 55 outliers final: 34 residues processed: 306 average time/residue: 0.1457 time to fit residues: 73.8872 Evaluate side-chains 275 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 709 CYS Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 1073 LEU Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 165 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 296 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 250 optimal weight: 0.0770 chunk 282 optimal weight: 0.6980 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN A 566 GLN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 GLN C1163 GLN D 55 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.153468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113014 restraints weight = 40829.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111785 restraints weight = 44745.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113120 restraints weight = 36850.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.113459 restraints weight = 25570.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.113728 restraints weight = 24098.286| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25154 Z= 0.139 Angle : 0.549 9.601 34278 Z= 0.289 Chirality : 0.044 0.273 3927 Planarity : 0.004 0.045 4433 Dihedral : 4.528 32.448 3412 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.64 % Allowed : 14.12 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.33 (0.14), residues: 3133 helix: 1.99 (0.21), residues: 649 sheet: -0.34 (0.19), residues: 689 loop : -1.03 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 365 TYR 0.029 0.001 TYR C 545 PHE 0.019 0.001 PHE C1019 TRP 0.015 0.001 TRP F 107 HIS 0.003 0.001 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00324 (25123) covalent geometry : angle 0.54714 (34216) SS BOND : bond 0.00284 ( 31) SS BOND : angle 1.25403 ( 62) hydrogen bonds : bond 0.04387 ( 950) hydrogen bonds : angle 5.62290 ( 2643) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 257 time to evaluate : 0.657 Fit side-chains REVERT: A 151 PHE cc_start: 0.7404 (m-80) cc_final: 0.7197 (m-80) REVERT: A 501 GLN cc_start: 0.6921 (mm-40) cc_final: 0.6616 (mm-40) REVERT: A 767 GLN cc_start: 0.6220 (tm-30) cc_final: 0.5972 (tm-30) REVERT: B 157 PHE cc_start: 0.7235 (m-10) cc_final: 0.7009 (m-10) REVERT: B 847 GLN cc_start: 0.8327 (tp40) cc_final: 0.8089 (pt0) REVERT: C 872 GLU cc_start: 0.8090 (tp30) cc_final: 0.7691 (tp30) REVERT: C 1133 ASP cc_start: 0.7948 (t0) cc_final: 0.7694 (t0) REVERT: C 1142 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8483 (ptm) REVERT: F 69 SER cc_start: 0.7466 (t) cc_final: 0.6990 (p) REVERT: F 81 MET cc_start: 0.2620 (mtm) cc_final: 0.2238 (mtm) REVERT: F 91 VAL cc_start: 0.6124 (OUTLIER) cc_final: 0.5752 (t) outliers start: 71 outliers final: 47 residues processed: 311 average time/residue: 0.1530 time to fit residues: 78.1012 Evaluate side-chains 291 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1097 GLN Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 709 CYS Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain C residue 1142 MET Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1196 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 242 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 267 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.109437 restraints weight = 40693.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108918 restraints weight = 32879.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110208 restraints weight = 24946.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.109977 restraints weight = 20958.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110212 restraints weight = 19616.822| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25154 Z= 0.176 Angle : 0.569 9.425 34278 Z= 0.298 Chirality : 0.045 0.205 3927 Planarity : 0.004 0.046 4433 Dihedral : 4.598 35.984 3412 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.94 % Allowed : 14.90 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.42 (0.14), residues: 3133 helix: 1.87 (0.20), residues: 654 sheet: -0.45 (0.19), residues: 700 loop : -1.05 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 365 TYR 0.028 0.001 TYR C 545 PHE 0.020 0.001 PHE C1019 TRP 0.015 0.001 TRP F 107 HIS 0.003 0.001 HIS C1150 Details of bonding type rmsd covalent geometry : bond 0.00418 (25123) covalent geometry : angle 0.56612 (34216) SS BOND : bond 0.00305 ( 31) SS BOND : angle 1.36369 ( 62) hydrogen bonds : bond 0.04520 ( 950) hydrogen bonds : angle 5.59454 ( 2643) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 256 time to evaluate : 0.901 Fit side-chains REVERT: A 501 GLN cc_start: 0.6934 (mm-40) cc_final: 0.6624 (mm-40) REVERT: B 157 PHE cc_start: 0.7185 (m-10) cc_final: 0.6943 (m-10) REVERT: B 194 ARG cc_start: 0.6958 (mtt180) cc_final: 0.6730 (mtm180) REVERT: B 847 GLN cc_start: 0.8345 (tp40) cc_final: 0.8078 (pt0) REVERT: B 855 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8424 (mp) REVERT: B 1042 ASP cc_start: 0.8013 (t70) cc_final: 0.7674 (t70) REVERT: C 475 SER cc_start: 0.8336 (t) cc_final: 0.7858 (p) REVERT: C 872 GLU cc_start: 0.8051 (tp30) cc_final: 0.7672 (tp30) REVERT: C 1073 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8049 (mp) REVERT: C 1142 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8427 (ptm) REVERT: F 81 MET cc_start: 0.2778 (mtm) cc_final: 0.2477 (mtm) REVERT: F 91 VAL cc_start: 0.6081 (OUTLIER) cc_final: 0.5685 (t) outliers start: 79 outliers final: 58 residues processed: 317 average time/residue: 0.1435 time to fit residues: 75.3231 Evaluate side-chains 302 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 240 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1097 GLN Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 709 CYS Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 1073 LEU Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain C residue 1142 MET Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1196 VAL Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 194 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** 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 = 0.3862 r_free = 0.3862 target = 0.152215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116350 restraints weight = 40865.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114509 restraints weight = 66986.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116867 restraints weight = 55902.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116887 restraints weight = 34176.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119401 restraints weight = 27811.819| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25154 Z= 0.172 Angle : 0.571 9.277 34278 Z= 0.299 Chirality : 0.045 0.369 3927 Planarity : 0.004 0.044 4433 Dihedral : 4.603 37.213 3412 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.87 % Allowed : 15.38 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.42 (0.14), residues: 3133 helix: 1.82 (0.20), residues: 655 sheet: -0.37 (0.19), residues: 694 loop : -1.07 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 19 TYR 0.029 0.001 TYR C 545 PHE 0.020 0.001 PHE C1019 TRP 0.016 0.001 TRP F 107 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00406 (25123) covalent geometry : angle 0.56886 (34216) SS BOND : bond 0.00351 ( 31) SS BOND : angle 1.36196 ( 62) hydrogen bonds : bond 0.04486 ( 950) hydrogen bonds : angle 5.53534 ( 2643) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 256 time to evaluate : 0.868 Fit side-chains REVERT: A 292 TYR cc_start: 0.7085 (m-80) cc_final: 0.6867 (t80) REVERT: A 501 GLN cc_start: 0.6921 (mm-40) cc_final: 0.6645 (mm-40) REVERT: B 157 PHE cc_start: 0.7217 (m-10) cc_final: 0.6960 (m-10) REVERT: B 194 ARG cc_start: 0.6944 (mtt180) cc_final: 0.6721 (mtm180) REVERT: B 390 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6703 (tm-30) REVERT: B 847 GLN cc_start: 0.8357 (tp40) cc_final: 0.8084 (pt0) REVERT: B 1042 ASP cc_start: 0.8052 (t70) cc_final: 0.7693 (t70) REVERT: C 475 SER cc_start: 0.8436 (t) cc_final: 0.8051 (p) REVERT: C 831 THR cc_start: 0.8814 (p) cc_final: 0.8446 (m) REVERT: C 872 GLU cc_start: 0.8079 (tp30) cc_final: 0.7690 (tp30) REVERT: C 1073 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8178 (mp) REVERT: C 1142 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8375 (ptm) REVERT: F 81 MET cc_start: 0.2672 (mtm) cc_final: 0.2420 (mtm) REVERT: F 91 VAL cc_start: 0.6097 (OUTLIER) cc_final: 0.5689 (t) outliers start: 77 outliers final: 56 residues processed: 314 average time/residue: 0.1431 time to fit residues: 74.6557 Evaluate side-chains 303 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1097 GLN Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 709 CYS Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 1073 LEU Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain C residue 1142 MET Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 71 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 133 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 141 optimal weight: 0.0980 chunk 51 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.151861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116194 restraints weight = 40865.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.115584 restraints weight = 70722.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117530 restraints weight = 55114.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117666 restraints weight = 34099.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119847 restraints weight = 28065.761| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25154 Z= 0.181 Angle : 0.582 9.216 34278 Z= 0.304 Chirality : 0.045 0.330 3927 Planarity : 0.004 0.046 4433 Dihedral : 4.643 37.560 3412 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.72 % Allowed : 16.05 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.48 (0.14), residues: 3133 helix: 1.77 (0.20), residues: 654 sheet: -0.43 (0.19), residues: 692 loop : -1.09 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 19 TYR 0.029 0.001 TYR C 545 PHE 0.030 0.001 PHE C 484 TRP 0.016 0.001 TRP F 107 HIS 0.004 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00430 (25123) covalent geometry : angle 0.57931 (34216) SS BOND : bond 0.00306 ( 31) SS BOND : angle 1.44007 ( 62) hydrogen bonds : bond 0.04538 ( 950) hydrogen bonds : angle 5.53459 ( 2643) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 253 time to evaluate : 0.906 Fit side-chains REVERT: A 501 GLN cc_start: 0.6900 (mm-40) cc_final: 0.6609 (mm-40) REVERT: B 157 PHE cc_start: 0.7216 (m-10) cc_final: 0.6961 (m-10) REVERT: B 390 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6622 (tm-30) REVERT: B 847 GLN cc_start: 0.8338 (tp40) cc_final: 0.8070 (pt0) REVERT: B 1042 ASP cc_start: 0.8056 (t70) cc_final: 0.7690 (t70) REVERT: C 475 SER cc_start: 0.8453 (t) cc_final: 0.8104 (p) REVERT: C 872 GLU cc_start: 0.8117 (tp30) cc_final: 0.7695 (tp30) REVERT: C 1073 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8194 (mp) REVERT: C 1142 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8392 (ptm) REVERT: C 1168 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8645 (m) REVERT: F 81 MET cc_start: 0.2734 (mtm) cc_final: 0.2494 (mtm) REVERT: F 91 VAL cc_start: 0.5981 (OUTLIER) cc_final: 0.5572 (t) outliers start: 73 outliers final: 57 residues processed: 306 average time/residue: 0.1398 time to fit residues: 70.4348 Evaluate side-chains 305 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 244 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1097 GLN Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 709 CYS Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 1073 LEU Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain C residue 1142 MET Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 251 optimal weight: 0.5980 chunk 34 optimal weight: 0.0470 overall best weight: 1.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.152164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116776 restraints weight = 40688.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116770 restraints weight = 68810.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118285 restraints weight = 53758.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118632 restraints weight = 33142.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121422 restraints weight = 27327.714| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25154 Z= 0.167 Angle : 0.573 8.979 34278 Z= 0.299 Chirality : 0.045 0.321 3927 Planarity : 0.004 0.043 4433 Dihedral : 4.603 36.929 3412 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.68 % Allowed : 16.20 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.45 (0.14), residues: 3133 helix: 1.85 (0.20), residues: 649 sheet: -0.43 (0.19), residues: 703 loop : -1.07 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 19 TYR 0.030 0.001 TYR C 545 PHE 0.027 0.001 PHE C 484 TRP 0.017 0.001 TRP F 107 HIS 0.004 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00394 (25123) covalent geometry : angle 0.57028 (34216) SS BOND : bond 0.00290 ( 31) SS BOND : angle 1.37039 ( 62) hydrogen bonds : bond 0.04453 ( 950) hydrogen bonds : angle 5.49185 ( 2643) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 254 time to evaluate : 0.958 Fit side-chains REVERT: A 292 TYR cc_start: 0.6681 (t80) cc_final: 0.6442 (t80) REVERT: A 501 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6638 (mm-40) REVERT: B 157 PHE cc_start: 0.7205 (m-10) cc_final: 0.6948 (m-10) REVERT: B 390 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6667 (tm-30) REVERT: B 847 GLN cc_start: 0.8325 (tp40) cc_final: 0.8068 (pt0) REVERT: B 965 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8572 (m-10) REVERT: B 1042 ASP cc_start: 0.8073 (t70) cc_final: 0.7700 (t70) REVERT: C 475 SER cc_start: 0.8476 (t) cc_final: 0.8158 (p) REVERT: C 872 GLU cc_start: 0.8108 (tp30) cc_final: 0.7693 (tp30) REVERT: C 1073 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8322 (mp) REVERT: C 1142 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8375 (ptm) REVERT: C 1168 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8628 (m) REVERT: F 81 MET cc_start: 0.2825 (mtm) cc_final: 0.2591 (mtm) REVERT: F 91 VAL cc_start: 0.5964 (OUTLIER) cc_final: 0.5545 (t) outliers start: 72 outliers final: 59 residues processed: 307 average time/residue: 0.1411 time to fit residues: 72.0398 Evaluate side-chains 307 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 243 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1097 GLN Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 709 CYS Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 1073 LEU Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain C residue 1142 MET Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 249 optimal weight: 0.7980 chunk 137 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 300 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 948 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.152265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116710 restraints weight = 40592.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116407 restraints weight = 69507.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118328 restraints weight = 53229.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118456 restraints weight = 33868.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120752 restraints weight = 27571.504| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25154 Z= 0.162 Angle : 0.574 9.098 34278 Z= 0.299 Chirality : 0.045 0.313 3927 Planarity : 0.004 0.043 4433 Dihedral : 4.574 36.601 3412 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.61 % Allowed : 16.72 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.44 (0.14), residues: 3133 helix: 1.86 (0.21), residues: 649 sheet: -0.42 (0.19), residues: 695 loop : -1.07 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 365 TYR 0.030 0.001 TYR C 545 PHE 0.025 0.001 PHE C 484 TRP 0.017 0.001 TRP F 107 HIS 0.003 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00384 (25123) covalent geometry : angle 0.57208 (34216) SS BOND : bond 0.00282 ( 31) SS BOND : angle 1.32376 ( 62) hydrogen bonds : bond 0.04409 ( 950) hydrogen bonds : angle 5.45893 ( 2643) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 248 time to evaluate : 0.819 Fit side-chains REVERT: A 292 TYR cc_start: 0.6809 (t80) cc_final: 0.6322 (t80) REVERT: A 501 GLN cc_start: 0.6883 (mm-40) cc_final: 0.6621 (mm-40) REVERT: A 825 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8205 (mtpt) REVERT: B 157 PHE cc_start: 0.7216 (m-10) cc_final: 0.6955 (m-10) REVERT: B 390 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6670 (tm-30) REVERT: B 705 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7973 (mm110) REVERT: B 847 GLN cc_start: 0.8317 (tp40) cc_final: 0.8061 (pt0) REVERT: B 965 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8583 (m-10) REVERT: B 1042 ASP cc_start: 0.8062 (t70) cc_final: 0.7687 (t70) REVERT: C 475 SER cc_start: 0.8492 (t) cc_final: 0.8192 (p) REVERT: C 872 GLU cc_start: 0.8116 (tp30) cc_final: 0.7690 (tp30) REVERT: C 1073 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8334 (mp) REVERT: C 1142 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8387 (ptm) REVERT: C 1168 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8633 (m) REVERT: F 81 MET cc_start: 0.2763 (mtm) cc_final: 0.2529 (mtm) REVERT: F 91 VAL cc_start: 0.5962 (OUTLIER) cc_final: 0.5590 (t) outliers start: 70 outliers final: 58 residues processed: 304 average time/residue: 0.1432 time to fit residues: 72.2344 Evaluate side-chains 306 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 241 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 705 GLN Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 709 CYS Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 1073 LEU Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain C residue 1142 MET Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1168 THR Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 258 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 202 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 141 optimal weight: 30.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** 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 = 0.3860 r_free = 0.3860 target = 0.152075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105684 restraints weight = 40864.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107016 restraints weight = 27112.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107213 restraints weight = 19904.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107261 restraints weight = 17561.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107472 restraints weight = 16794.569| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25154 Z= 0.173 Angle : 0.579 9.105 34278 Z= 0.302 Chirality : 0.045 0.310 3927 Planarity : 0.004 0.044 4433 Dihedral : 4.599 36.960 3412 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.64 % Allowed : 16.54 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.47 (0.14), residues: 3133 helix: 1.84 (0.20), residues: 649 sheet: -0.43 (0.19), residues: 692 loop : -1.09 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 365 TYR 0.030 0.001 TYR C 545 PHE 0.026 0.001 PHE A 657 TRP 0.015 0.001 TRP F 107 HIS 0.003 0.001 HIS C1150 Details of bonding type rmsd covalent geometry : bond 0.00411 (25123) covalent geometry : angle 0.57605 (34216) SS BOND : bond 0.00383 ( 31) SS BOND : angle 1.51657 ( 62) hydrogen bonds : bond 0.04450 ( 950) hydrogen bonds : angle 5.46446 ( 2643) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3593.75 seconds wall clock time: 63 minutes 9.37 seconds (3789.37 seconds total)