Starting phenix.real_space_refine on Mon Feb 19 11:53:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9b_24255/02_2024/7n9b_24255.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9b_24255/02_2024/7n9b_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_2024/7n9b_24255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9b_24255/02_2024/7n9b_24255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9b_24255/02_2024/7n9b_24255.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9b_24255/02_2024/7n9b_24255.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12.84, per 1000 atoms: 0.52 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: 10.01 Conformation dependent library (CDL) restraints added in 4.5 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: 3.21 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: 11.75 Time building geometry restraints manager: 10.60 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 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: 8.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 31.230 Check model and map are aligned: 0.340 Set scattering table: 0.240 Process input model: 69.110 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.650 ------------------------------------------------------------------------------- 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 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 % 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 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP B 978 HIS 0.008 0.002 HIS B1140 PHE 0.059 0.003 PHE D 45 TYR 0.057 0.004 TYR C 581 ARG 0.036 0.001 ARG F 31 *********************** 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 : 2.613 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: 0.7432 (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: 0.2147 (mpp) cc_final: 0.1784 (mtm) outliers start: 2 outliers final: 2 residues processed: 300 average time/residue: 0.3298 time to fit residues: 161.2228 Evaluate side-chains 242 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 2.741 ------------------------------------------------------------------------------- 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 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: 0.7981 moved from start: 0.1248 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= 0.210 Angle : 0.623 10.102 34216 Z= 0.332 Chirality : 0.046 0.169 3927 Planarity : 0.005 0.044 4433 Dihedral : 4.848 25.730 3413 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.08 % Allowed : 11.25 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.35 (0.14), residues: 3133 helix: 2.06 (0.20), residues: 651 sheet: -0.23 (0.19), residues: 698 loop : -1.14 (0.13), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 34 HIS 0.006 0.001 HIS D 30 PHE 0.019 0.001 PHE C 657 TYR 0.022 0.002 TYR C 545 ARG 0.006 0.001 ARG C 365 *********************** 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 320 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 291 time to evaluate : 2.982 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.5965 (mm-30) cc_final: 0.5671 (mm-30) REVERT: B 157 PHE cc_start: 0.7277 (m-10) cc_final: 0.6841 (m-10) REVERT: B 287 LYS cc_start: 0.8363 (pttt) cc_final: 0.8081 (pttm) REVERT: B 1042 ASP cc_start: 0.8080 (t70) cc_final: 0.7627 (t70) REVERT: C 600 TYR cc_start: 0.8142 (m-80) cc_final: 0.7418 (m-80) REVERT: C 872 GLU cc_start: 0.8160 (tp30) cc_final: 0.7677 (tp30) REVERT: C 1133 ASP cc_start: 0.7902 (t0) cc_final: 0.7557 (t0) REVERT: D 81 MET cc_start: 0.5126 (mtt) cc_final: 0.4519 (ptt) REVERT: F 69 SER cc_start: 0.7465 (t) cc_final: 0.6955 (p) REVERT: F 81 MET cc_start: 0.2202 (mpp) cc_final: 0.1623 (mtm) outliers start: 29 outliers final: 18 residues processed: 305 average time/residue: 0.3362 time to fit residues: 168.2625 Evaluate side-chains 266 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 248 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 VAL 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 A residue 639 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 737 THR 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 319 VAL Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 285 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 230 optimal weight: 0.0020 overall best weight: 1.5994 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25123 Z= 0.245 Angle : 0.578 10.399 34216 Z= 0.304 Chirality : 0.045 0.321 3927 Planarity : 0.004 0.045 4433 Dihedral : 4.694 27.095 3412 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.12 % Allowed : 13.00 % Favored : 84.88 % 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: -0.40 (0.14), residues: 3133 helix: 1.96 (0.20), residues: 648 sheet: -0.32 (0.19), residues: 703 loop : -1.12 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 34 HIS 0.005 0.001 HIS C 141 PHE 0.018 0.001 PHE A 657 TYR 0.026 0.001 TYR C 545 ARG 0.007 0.000 ARG C 365 *********************** 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 323 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 266 time to evaluate : 2.749 Fit side-chains REVERT: A 188 GLU cc_start: 0.5958 (mm-30) cc_final: 0.5724 (mm-30) REVERT: A 492 PHE cc_start: 0.8215 (p90) cc_final: 0.7968 (p90) REVERT: A 581 TYR cc_start: 0.6983 (m-10) cc_final: 0.6740 (m-80) REVERT: B 157 PHE cc_start: 0.7242 (m-10) cc_final: 0.6829 (m-10) REVERT: B 287 LYS cc_start: 0.8474 (pttt) cc_final: 0.8171 (pttm) REVERT: B 742 LEU cc_start: 0.8930 (tp) cc_final: 0.8727 (mp) REVERT: B 847 GLN cc_start: 0.8511 (tp40) cc_final: 0.8037 (pt0) REVERT: B 1042 ASP cc_start: 0.8124 (t70) cc_final: 0.7704 (t70) REVERT: C 180 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: C 484 PHE cc_start: 0.7746 (m-80) cc_final: 0.7482 (m-80) REVERT: C 872 GLU cc_start: 0.8176 (tp30) cc_final: 0.7737 (tp30) REVERT: C 1133 ASP cc_start: 0.7895 (t0) cc_final: 0.7526 (t0) REVERT: D 81 MET cc_start: 0.5107 (mtt) cc_final: 0.4479 (ptt) REVERT: F 20 LEU cc_start: 0.5042 (OUTLIER) cc_final: 0.4788 (mm) REVERT: F 69 SER cc_start: 0.7431 (t) cc_final: 0.6899 (p) outliers start: 57 outliers final: 33 residues processed: 305 average time/residue: 0.3782 time to fit residues: 188.1095 Evaluate side-chains 279 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 244 time to evaluate : 2.737 ------------------------------------------------------------------------------- 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 332 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 A residue 1169 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 587 TYR 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 180 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 709 CYS Chi-restraints excluded: chain C residue 1132 VAL 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 Chi-restraints excluded: chain F residue 20 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 273 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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** C 141 HIS C 406 GLN ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 GLN ** C1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25123 Z= 0.275 Angle : 0.576 10.519 34216 Z= 0.301 Chirality : 0.045 0.236 3927 Planarity : 0.004 0.046 4433 Dihedral : 4.676 33.059 3412 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.50 % Allowed : 14.64 % Favored : 82.87 % 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: -0.49 (0.14), residues: 3133 helix: 1.83 (0.20), residues: 654 sheet: -0.41 (0.19), residues: 679 loop : -1.14 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 107 HIS 0.005 0.001 HIS C 141 PHE 0.020 0.001 PHE A 184 TYR 0.027 0.001 TYR C 545 ARG 0.005 0.000 ARG D 19 *********************** 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 327 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 260 time to evaluate : 2.727 Fit side-chains REVERT: A 188 GLU cc_start: 0.5918 (mm-30) cc_final: 0.5664 (mm-30) REVERT: A 501 GLN cc_start: 0.6922 (mm-40) cc_final: 0.6588 (mm-40) REVERT: A 767 GLN cc_start: 0.6431 (tm-30) cc_final: 0.6016 (tm-30) REVERT: B 157 PHE cc_start: 0.7317 (m-10) cc_final: 0.6881 (m-10) REVERT: B 194 ARG cc_start: 0.7130 (mtt180) cc_final: 0.6853 (mtm180) REVERT: B 287 LYS cc_start: 0.8471 (pttt) cc_final: 0.8138 (pttm) REVERT: B 847 GLN cc_start: 0.8493 (tp40) cc_final: 0.8050 (pt0) REVERT: B 1042 ASP cc_start: 0.8142 (t70) cc_final: 0.7732 (t70) REVERT: C 180 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6934 (m-30) REVERT: C 361 TYR cc_start: 0.7992 (m-10) cc_final: 0.7785 (m-10) REVERT: C 484 PHE cc_start: 0.7818 (m-80) cc_final: 0.7603 (m-80) REVERT: C 872 GLU cc_start: 0.8163 (tp30) cc_final: 0.7739 (tp30) REVERT: C 1073 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8003 (mp) REVERT: C 1133 ASP cc_start: 0.7867 (t0) cc_final: 0.7527 (t0) REVERT: D 81 MET cc_start: 0.4934 (mtt) cc_final: 0.4472 (ptt) REVERT: F 69 SER cc_start: 0.7482 (t) cc_final: 0.6914 (p) REVERT: F 91 VAL cc_start: 0.6556 (OUTLIER) cc_final: 0.6179 (t) outliers start: 67 outliers final: 47 residues processed: 310 average time/residue: 0.3416 time to fit residues: 173.8387 Evaluate side-chains 295 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 245 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 191 ASN 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 332 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 639 THR 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 1169 THR Chi-restraints excluded: chain B residue 218 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 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 180 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 520 ASP 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 1143 SER Chi-restraints excluded: chain C residue 1196 VAL 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 91 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 0.9990 chunk 173 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 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: 6.9990 chunk 274 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 876 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 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25123 Z= 0.215 Angle : 0.538 9.788 34216 Z= 0.282 Chirality : 0.044 0.204 3927 Planarity : 0.004 0.043 4433 Dihedral : 4.539 34.975 3412 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.91 % Allowed : 14.93 % 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 (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: 1.98 (0.20), residues: 655 sheet: -0.42 (0.19), residues: 683 loop : -1.06 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 107 HIS 0.003 0.001 HIS A 611 PHE 0.018 0.001 PHE C1019 TYR 0.029 0.001 TYR C 545 ARG 0.005 0.000 ARG D 19 *********************** 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 335 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 257 time to evaluate : 2.848 Fit side-chains revert: symmetry clash REVERT: A 501 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6626 (mm-40) REVERT: A 767 GLN cc_start: 0.6351 (tm-30) cc_final: 0.5965 (tm-30) REVERT: B 157 PHE cc_start: 0.7278 (m-10) cc_final: 0.6896 (m-10) REVERT: B 847 GLN cc_start: 0.8465 (tp40) cc_final: 0.8033 (pt0) REVERT: C 361 TYR cc_start: 0.7947 (m-10) cc_final: 0.7740 (m-10) REVERT: C 600 TYR cc_start: 0.7904 (m-80) cc_final: 0.7413 (m-80) REVERT: C 831 THR cc_start: 0.8869 (p) cc_final: 0.8579 (m) REVERT: C 872 GLU cc_start: 0.8167 (tp30) cc_final: 0.7771 (tp30) REVERT: C 1073 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.7989 (mp) REVERT: C 1133 ASP cc_start: 0.7862 (t0) cc_final: 0.7519 (t0) REVERT: C 1142 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8492 (ptm) REVERT: D 81 MET cc_start: 0.4804 (mtt) cc_final: 0.4287 (ptt) REVERT: F 91 VAL cc_start: 0.6430 (OUTLIER) cc_final: 0.6044 (t) outliers start: 78 outliers final: 55 residues processed: 319 average time/residue: 0.3377 time to fit residues: 176.3928 Evaluate side-chains 305 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 247 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 191 ASN 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 332 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 474 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 639 THR 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 1051 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 218 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 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 188 GLU 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 520 ASP Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 691 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 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 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 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 102 optimal weight: 0.0980 chunk 275 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 305 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 160 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25123 Z= 0.189 Angle : 0.531 9.346 34216 Z= 0.276 Chirality : 0.044 0.343 3927 Planarity : 0.004 0.042 4433 Dihedral : 4.426 34.120 3412 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.05 % Allowed : 15.87 % Favored : 81.08 % 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: -0.30 (0.15), residues: 3133 helix: 2.02 (0.20), residues: 661 sheet: -0.31 (0.19), residues: 677 loop : -1.03 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 107 HIS 0.003 0.001 HIS A 611 PHE 0.029 0.001 PHE C 484 TYR 0.028 0.001 TYR C 545 ARG 0.004 0.000 ARG B 857 *********************** 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 340 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 258 time to evaluate : 2.680 Fit side-chains REVERT: A 292 TYR cc_start: 0.7443 (m-80) cc_final: 0.7025 (t80) REVERT: A 501 GLN cc_start: 0.6991 (mm-40) cc_final: 0.6664 (mm-40) REVERT: A 767 GLN cc_start: 0.6312 (tm-30) cc_final: 0.5926 (tm-30) REVERT: B 157 PHE cc_start: 0.7277 (m-10) cc_final: 0.6925 (m-10) REVERT: B 390 GLU cc_start: 0.6985 (tt0) cc_final: 0.6748 (tm-30) REVERT: B 847 GLN cc_start: 0.8457 (tp40) cc_final: 0.8040 (pt0) REVERT: C 600 TYR cc_start: 0.7858 (m-80) cc_final: 0.7563 (m-80) REVERT: C 831 THR cc_start: 0.8862 (p) cc_final: 0.8624 (m) REVERT: C 872 GLU cc_start: 0.8183 (tp30) cc_final: 0.7822 (tp30) REVERT: C 1073 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.7958 (mp) REVERT: C 1133 ASP cc_start: 0.7872 (t0) cc_final: 0.7536 (t0) REVERT: C 1142 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8519 (ptm) REVERT: D 81 MET cc_start: 0.4980 (mtt) cc_final: 0.4476 (ptt) REVERT: D 85 LYS cc_start: 0.6860 (mmpt) cc_final: 0.6521 (ptmt) REVERT: F 91 VAL cc_start: 0.6432 (OUTLIER) cc_final: 0.6047 (t) outliers start: 82 outliers final: 61 residues processed: 322 average time/residue: 0.3242 time to fit residues: 170.9656 Evaluate side-chains 307 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 243 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 191 ASN 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 332 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 639 THR Chi-restraints excluded: chain A residue 643 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 969 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 218 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 707 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 742 LEU 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 154 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 691 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 304 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 598 GLN A 782 GLN ** A1146 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 ** 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: 0.8090 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 25123 Z= 0.519 Angle : 0.691 9.910 34216 Z= 0.364 Chirality : 0.049 0.300 3927 Planarity : 0.005 0.067 4433 Dihedral : 5.128 44.027 3412 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.84 % Allowed : 15.72 % Favored : 80.45 % 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: -0.91 (0.14), residues: 3133 helix: 1.27 (0.20), residues: 654 sheet: -0.53 (0.18), residues: 709 loop : -1.39 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 978 HIS 0.009 0.002 HIS D 30 PHE 0.025 0.002 PHE C 484 TYR 0.030 0.002 TYR C 545 ARG 0.012 0.001 ARG D 19 *********************** 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 358 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 255 time to evaluate : 2.696 Fit side-chains REVERT: A 292 TYR cc_start: 0.7572 (m-80) cc_final: 0.6963 (t80) REVERT: A 767 GLN cc_start: 0.6388 (tm-30) cc_final: 0.5973 (tm-30) REVERT: B 157 PHE cc_start: 0.7403 (m-10) cc_final: 0.6958 (m-10) REVERT: B 187 THR cc_start: 0.7771 (p) cc_final: 0.7531 (t) REVERT: B 847 GLN cc_start: 0.8518 (tp40) cc_final: 0.8015 (pt0) REVERT: B 855 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 1042 ASP cc_start: 0.8191 (t70) cc_final: 0.7760 (t70) REVERT: B 1088 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8765 (mp) REVERT: C 180 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6902 (m-30) REVERT: C 872 GLU cc_start: 0.8251 (tp30) cc_final: 0.7901 (tp30) REVERT: C 1133 ASP cc_start: 0.7938 (t0) cc_final: 0.7671 (t0) REVERT: C 1168 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8723 (m) REVERT: F 91 VAL cc_start: 0.6264 (OUTLIER) cc_final: 0.5866 (t) outliers start: 103 outliers final: 73 residues processed: 330 average time/residue: 0.3232 time to fit residues: 176.0494 Evaluate side-chains 320 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 242 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 191 ASN 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 332 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 481 ASP Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 684 PHE 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 1051 LEU Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 218 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 707 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 855 LEU 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 1077 ASP Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1097 GLN Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain B residue 1224 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 533 LEU 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 691 THR 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 1132 VAL 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 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 188 optimal weight: 0.5980 chunk 121 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 193 optimal weight: 0.0050 chunk 207 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 239 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 782 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** C1163 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25123 Z= 0.156 Angle : 0.539 8.857 34216 Z= 0.280 Chirality : 0.044 0.276 3927 Planarity : 0.004 0.044 4433 Dihedral : 4.558 36.996 3412 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.86 % Allowed : 18.14 % Favored : 80.00 % 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: -0.44 (0.14), residues: 3133 helix: 1.92 (0.20), residues: 656 sheet: -0.47 (0.19), residues: 689 loop : -1.10 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 107 HIS 0.004 0.001 HIS D 30 PHE 0.021 0.001 PHE C 484 TYR 0.028 0.001 TYR C 545 ARG 0.005 0.000 ARG A1111 *********************** 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 317 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 267 time to evaluate : 2.782 Fit side-chains REVERT: A 292 TYR cc_start: 0.7503 (m-80) cc_final: 0.7080 (t80) REVERT: A 501 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6677 (mm-40) REVERT: B 157 PHE cc_start: 0.7313 (m-10) cc_final: 0.6936 (m-10) REVERT: B 847 GLN cc_start: 0.8421 (tp40) cc_final: 0.8058 (pt0) REVERT: C 600 TYR cc_start: 0.7713 (m-80) cc_final: 0.7484 (m-80) REVERT: C 831 THR cc_start: 0.8828 (p) cc_final: 0.8565 (m) REVERT: C 872 GLU cc_start: 0.8213 (tp30) cc_final: 0.7842 (tp30) REVERT: C 1133 ASP cc_start: 0.7883 (t0) cc_final: 0.7518 (t0) REVERT: D 85 LYS cc_start: 0.6632 (mmpt) cc_final: 0.6066 (ptmt) REVERT: F 91 VAL cc_start: 0.6382 (OUTLIER) cc_final: 0.5961 (t) outliers start: 50 outliers final: 38 residues processed: 304 average time/residue: 0.3340 time to fit residues: 166.6773 Evaluate side-chains 287 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 248 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 ILE 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 639 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 218 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 587 TYR 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 1132 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 691 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 1132 VAL Chi-restraints excluded: chain C residue 1196 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE 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 291 optimal weight: 0.2980 chunk 266 optimal weight: 6.9990 chunk 283 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 222 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 256 optimal weight: 0.3980 chunk 268 optimal weight: 0.9980 chunk 282 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** A1047 ASN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN B 993 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25123 Z= 0.161 Angle : 0.524 9.185 34216 Z= 0.271 Chirality : 0.043 0.265 3927 Planarity : 0.004 0.044 4433 Dihedral : 4.340 33.523 3412 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.01 % Allowed : 18.06 % Favored : 79.93 % 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: 2.05 (0.20), residues: 661 sheet: -0.39 (0.18), residues: 703 loop : -1.03 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 34 HIS 0.004 0.001 HIS D 30 PHE 0.022 0.001 PHE C1019 TYR 0.027 0.001 TYR C 545 ARG 0.004 0.000 ARG A1111 *********************** 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 304 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 250 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 TYR cc_start: 0.7464 (m-80) cc_final: 0.7032 (t80) REVERT: A 501 GLN cc_start: 0.6959 (mm-40) cc_final: 0.6672 (mm-40) REVERT: B 157 PHE cc_start: 0.7264 (m-10) cc_final: 0.6923 (m-10) REVERT: B 847 GLN cc_start: 0.8397 (tp40) cc_final: 0.8047 (pt0) REVERT: B 1088 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8723 (mt) REVERT: C 831 THR cc_start: 0.8867 (p) cc_final: 0.8643 (m) REVERT: C 872 GLU cc_start: 0.8225 (tp30) cc_final: 0.7855 (tp30) REVERT: C 1073 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8153 (mp) REVERT: C 1133 ASP cc_start: 0.7927 (t0) cc_final: 0.7586 (t0) REVERT: F 91 VAL cc_start: 0.6403 (OUTLIER) cc_final: 0.5979 (t) outliers start: 54 outliers final: 43 residues processed: 290 average time/residue: 0.3303 time to fit residues: 157.6686 Evaluate side-chains 286 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 240 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 218 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 587 TYR 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 1008 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 691 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 1233 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE 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 300 optimal weight: 0.0470 chunk 183 optimal weight: 0.5980 chunk 142 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 314 optimal weight: 10.0000 chunk 289 optimal weight: 0.7980 chunk 250 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 193 optimal weight: 0.0980 chunk 153 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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** C 501 GLN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 948 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25123 Z= 0.142 Angle : 0.521 9.807 34216 Z= 0.269 Chirality : 0.043 0.317 3927 Planarity : 0.004 0.047 4433 Dihedral : 4.245 31.428 3412 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.86 % Allowed : 18.40 % Favored : 79.74 % 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: -0.21 (0.15), residues: 3133 helix: 2.17 (0.21), residues: 656 sheet: -0.36 (0.18), residues: 718 loop : -0.95 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 34 HIS 0.010 0.001 HIS D 30 PHE 0.023 0.001 PHE C1019 TYR 0.030 0.001 TYR C 600 ARG 0.005 0.000 ARG C 365 ********************** 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 300 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 250 time to evaluate : 3.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 TYR cc_start: 0.7437 (m-80) cc_final: 0.7029 (t80) REVERT: A 501 GLN cc_start: 0.6986 (mm-40) cc_final: 0.6711 (mm-40) REVERT: B 157 PHE cc_start: 0.7227 (m-10) cc_final: 0.6936 (m-10) REVERT: B 194 ARG cc_start: 0.6990 (mtt180) cc_final: 0.6712 (mtm180) REVERT: B 847 GLN cc_start: 0.8373 (tp40) cc_final: 0.8040 (pt0) REVERT: B 965 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8522 (m-10) REVERT: C 513 TYR cc_start: 0.5813 (m-10) cc_final: 0.5517 (m-10) REVERT: C 831 THR cc_start: 0.8870 (p) cc_final: 0.8656 (m) REVERT: C 872 GLU cc_start: 0.8234 (tp30) cc_final: 0.7874 (tp30) REVERT: C 1073 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8159 (mp) REVERT: C 1133 ASP cc_start: 0.7935 (t0) cc_final: 0.7594 (t0) REVERT: C 1168 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8763 (m) REVERT: F 91 VAL cc_start: 0.6431 (OUTLIER) cc_final: 0.6017 (t) outliers start: 50 outliers final: 41 residues processed: 289 average time/residue: 0.3295 time to fit residues: 157.3004 Evaluate side-chains 283 residues out of total 2780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 238 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 218 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 587 TYR 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 853 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 187 THR Chi-restraints excluded: chain C residue 188 GLU 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 691 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 1168 THR Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE 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 267 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 231 optimal weight: 0.0670 chunk 37 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 overall best weight: 1.0124 ------------------------------------------------------------------------------- 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 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** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** 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 = 0.3891 r_free = 0.3891 target = 0.154593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119334 restraints weight = 40844.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119880 restraints weight = 65902.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121342 restraints weight = 51381.743| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2695 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= 0.178 Angle : 0.533 11.868 34216 Z= 0.273 Chirality : 0.044 0.328 3927 Planarity : 0.004 0.045 4433 Dihedral : 4.218 30.747 3412 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.94 % Allowed : 18.36 % Favored : 79.70 % 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: -0.21 (0.15), residues: 3133 helix: 2.15 (0.21), residues: 655 sheet: -0.33 (0.18), residues: 717 loop : -0.95 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 34 HIS 0.003 0.001 HIS C1156 PHE 0.023 0.001 PHE A 232 TYR 0.029 0.001 TYR C 545 ARG 0.005 0.000 ARG C 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4831.01 seconds wall clock time: 89 minutes 50.42 seconds (5390.42 seconds total)