Starting phenix.real_space_refine (version: dev) on Sat Feb 25 03:53:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9b_24255/02_2023/7n9b_24255.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9b_24255/02_2023/7n9b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9b_24255/02_2023/7n9b_24255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9b_24255/02_2023/7n9b_24255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9b_24255/02_2023/7n9b_24255.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9b_24255/02_2023/7n9b_24255.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A ASP 145": "OD1" <-> "OD2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 911": "OE1" <-> "OE2" Residue "A GLU 1109": "OE1" <-> "OE2" Residue "A PHE 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 666": "OD1" <-> "OD2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 888": "OD1" <-> "OD2" Residue "C GLU 911": "OE1" <-> "OE2" Residue "C ASP 1133": "OD1" <-> "OD2" Residue "C PHE 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/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: {'PHE:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 6} 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: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG: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: {'PHE:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} 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: 13.45, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.19 Conformation dependent library (CDL) restraints added in 3.7 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: 2.08 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: 12.36 Time building geometry restraints manager: 10.78 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: 95.48 - 104.36: 502 104.36 - 113.24: 13466 113.24 - 122.12: 16133 122.12 - 131.00: 4062 131.00 - 139.88: 53 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 2.440 nonbonded pdb=" O THR A 485 " pdb=" OG1 THR A 615 " model vdw 2.203 2.440 nonbonded pdb=" O ASP A 386 " pdb=" OG SER A 389 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR C 129 " pdb=" O LEU C 146 " model vdw 2.227 2.440 nonbonded pdb=" OE1 GLN D 1 " pdb=" OH TYR D 106 " model vdw 2.254 2.440 ... (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 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 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. 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: 6.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 30.370 Check model and map are aligned: 0.460 Process input model: 67.290 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.230 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 25123 Z= 0.876 Angle : 1.411 24.418 34216 Z= 0.988 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 : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (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 *********************** 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 fitting. rotamer outliers: 2 poor density : 298 time to evaluate : 3.095 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 300 average time/residue: 0.3553 time to fit residues: 173.6539 Evaluate side-chains 241 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 239 time to evaluate : 3.031 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2408 time to fit residues: 5.2690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 0.2980 chunk 239 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 286 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 540 ASN A 542 ASN A 993 GLN A1047 ASN A1198 GLN A1234 GLN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** 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** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 25123 Z= 0.204 Angle : 0.622 10.253 34216 Z= 0.330 Chirality : 0.046 0.173 3927 Planarity : 0.005 0.045 4433 Dihedral : 4.859 25.856 3411 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3133 helix: 2.04 (0.20), residues: 656 sheet: -0.22 (0.19), residues: 698 loop : -1.13 (0.13), residues: 1779 *********************** 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 321 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 294 time to evaluate : 3.200 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 306 average time/residue: 0.3569 time to fit residues: 178.2335 Evaluate side-chains 258 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 242 time to evaluate : 3.030 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2268 time to fit residues: 11.2272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 238 optimal weight: 0.0470 chunk 195 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 287 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 230 optimal weight: 0.0040 overall best weight: 1.5894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN A 767 GLN A 876 GLN A1097 GLN A1166 ASN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** 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 ** C1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 25123 Z= 0.239 Angle : 0.580 10.354 34216 Z= 0.305 Chirality : 0.045 0.307 3927 Planarity : 0.004 0.045 4433 Dihedral : 4.671 23.334 3411 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3133 helix: 1.92 (0.20), residues: 659 sheet: -0.32 (0.19), residues: 682 loop : -1.10 (0.14), residues: 1792 *********************** 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 316 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 268 time to evaluate : 3.166 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 22 residues processed: 304 average time/residue: 0.3743 time to fit residues: 186.8492 Evaluate side-chains 264 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 242 time to evaluate : 3.043 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2334 time to fit residues: 13.9710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 137 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 305 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 273 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS C 406 GLN ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 25123 Z= 0.247 Angle : 0.567 10.207 34216 Z= 0.296 Chirality : 0.045 0.236 3927 Planarity : 0.004 0.045 4433 Dihedral : 4.628 32.167 3411 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3133 helix: 1.90 (0.20), residues: 655 sheet: -0.34 (0.19), residues: 664 loop : -1.11 (0.14), residues: 1814 *********************** 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 303 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 262 time to evaluate : 3.133 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 21 residues processed: 291 average time/residue: 0.3559 time to fit residues: 169.7294 Evaluate side-chains 257 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 236 time to evaluate : 3.030 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2338 time to fit residues: 13.7299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 260 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 274 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN A 767 GLN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 25123 Z= 0.309 Angle : 0.581 10.066 34216 Z= 0.305 Chirality : 0.045 0.238 3927 Planarity : 0.004 0.045 4433 Dihedral : 4.685 29.722 3411 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3133 helix: 1.84 (0.20), residues: 647 sheet: -0.52 (0.18), residues: 701 loop : -1.18 (0.14), residues: 1785 *********************** 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 291 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 246 time to evaluate : 2.969 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 20 residues processed: 280 average time/residue: 0.3420 time to fit residues: 157.5479 Evaluate side-chains 256 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 236 time to evaluate : 3.075 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2607 time to fit residues: 14.0957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 25123 Z= 0.168 Angle : 0.537 9.410 34216 Z= 0.278 Chirality : 0.044 0.378 3927 Planarity : 0.004 0.041 4433 Dihedral : 4.434 30.959 3411 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3133 helix: 2.04 (0.21), residues: 655 sheet: -0.34 (0.19), residues: 689 loop : -1.06 (0.14), residues: 1789 *********************** 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 296 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 269 time to evaluate : 3.018 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 288 average time/residue: 0.3668 time to fit residues: 173.2217 Evaluate side-chains 252 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 239 time to evaluate : 2.627 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2160 time to fit residues: 9.3680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 172 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 304 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 140 optimal weight: 0.0270 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN A 767 GLN A1047 ASN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 25123 Z= 0.274 Angle : 0.571 9.459 34216 Z= 0.298 Chirality : 0.045 0.327 3927 Planarity : 0.004 0.045 4433 Dihedral : 4.530 28.640 3411 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3133 helix: 1.90 (0.20), residues: 655 sheet: -0.38 (0.19), residues: 695 loop : -1.12 (0.14), residues: 1783 *********************** 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 279 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 248 time to evaluate : 3.034 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 268 average time/residue: 0.3735 time to fit residues: 163.7326 Evaluate side-chains 250 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 236 time to evaluate : 2.936 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2487 time to fit residues: 10.7161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 193 optimal weight: 0.0980 chunk 207 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 239 optimal weight: 0.5980 chunk 277 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 767 GLN A1047 ASN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 25123 Z= 0.172 Angle : 0.539 9.078 34216 Z= 0.278 Chirality : 0.044 0.297 3927 Planarity : 0.004 0.041 4433 Dihedral : 4.378 29.535 3411 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3133 helix: 2.06 (0.21), residues: 654 sheet: -0.38 (0.19), residues: 705 loop : -1.04 (0.14), residues: 1774 *********************** 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 273 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 254 time to evaluate : 2.870 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 264 average time/residue: 0.3857 time to fit residues: 166.7997 Evaluate side-chains 247 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 239 time to evaluate : 3.134 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2648 time to fit residues: 8.0697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 0.9980 chunk 266 optimal weight: 4.9990 chunk 283 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 268 optimal weight: 0.3980 chunk 282 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 25123 Z= 0.193 Angle : 0.541 9.042 34216 Z= 0.279 Chirality : 0.044 0.285 3927 Planarity : 0.004 0.041 4433 Dihedral : 4.350 31.011 3411 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3133 helix: 2.06 (0.21), residues: 654 sheet: -0.35 (0.18), residues: 713 loop : -1.05 (0.14), residues: 1766 *********************** 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 259 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 245 time to evaluate : 2.865 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 254 average time/residue: 0.3813 time to fit residues: 156.9294 Evaluate side-chains 242 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 235 time to evaluate : 2.893 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2612 time to fit residues: 7.5109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 314 optimal weight: 5.9990 chunk 289 optimal weight: 0.8980 chunk 250 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 193 optimal weight: 0.3980 chunk 153 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN A 782 GLN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 25123 Z= 0.170 Angle : 0.536 9.222 34216 Z= 0.276 Chirality : 0.044 0.351 3927 Planarity : 0.004 0.041 4433 Dihedral : 4.265 27.955 3411 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3133 helix: 2.18 (0.21), residues: 648 sheet: -0.42 (0.19), residues: 694 loop : -0.99 (0.14), residues: 1791 ********************** 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 262 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 251 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 254 average time/residue: 0.3847 time to fit residues: 160.4840 Evaluate side-chains 246 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 239 time to evaluate : 2.855 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2500 time to fit residues: 7.3511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 231 optimal weight: 9.9990 chunk 37 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 31 optimal weight: 0.0070 chunk 46 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.156026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120993 restraints weight = 40733.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120746 restraints weight = 66524.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122587 restraints weight = 53528.588| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 25123 Z= 0.146 Angle : 0.523 9.467 34216 Z= 0.269 Chirality : 0.043 0.312 3927 Planarity : 0.004 0.043 4433 Dihedral : 4.171 26.220 3411 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3133 helix: 2.15 (0.21), residues: 657 sheet: -0.31 (0.18), residues: 718 loop : -0.94 (0.14), residues: 1758 =============================================================================== Job complete usr+sys time: 4536.37 seconds wall clock time: 84 minutes 57.07 seconds (5097.07 seconds total)