Starting phenix.real_space_refine on Sun Dec 29 06:11:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fsj_29419/12_2024/8fsj_29419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fsj_29419/12_2024/8fsj_29419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fsj_29419/12_2024/8fsj_29419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fsj_29419/12_2024/8fsj_29419.map" model { file = "/net/cci-nas-00/data/ceres_data/8fsj_29419/12_2024/8fsj_29419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fsj_29419/12_2024/8fsj_29419.cif" } resolution = 3.65 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= 0.021 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 51 5.16 5 C 6166 2.51 5 N 1642 2.21 5 O 1996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9855 Number of models: 1 Model: "" Number of chains: 16 Chain: "E" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2235 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 260} Chain: "H" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1638 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1629 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 631 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 6, 'TRANS': 75} Chain breaks: 1 Chain: "B" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1556 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1792 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.53, per 1000 atoms: 0.66 Number of scatterers: 9855 At special positions: 0 Unit cell: (74.676, 135.128, 137.795, 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 51 16.00 O 1996 8.00 N 1642 7.00 C 6166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS E 429 " - pdb=" SG CYS E 503 " distance=2.05 Simple disulfide: pdb=" SG CYS E 452 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 459 " - pdb=" SG CYS E 486 " distance=2.03 Simple disulfide: pdb=" SG CYS E 494 " - pdb=" SG CYS E 564 " distance=2.04 Simple disulfide: pdb=" SG CYS E 508 " - pdb=" SG CYS E 552 " distance=2.03 Simple disulfide: pdb=" SG CYS E 569 " - pdb=" SG CYS E 597 " distance=2.03 Simple disulfide: pdb=" SG CYS E 581 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 607 " - pdb=" SG CYS E 644 " distance=2.04 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 677 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 401 " - " ASN A 209 " " NAG A 402 " - " ASN A 250 " " NAG D 1 " - " ASN E 430 " " NAG E 801 " - " ASN E 576 " " NAG E 802 " - " ASN E 695 " " NAG E 803 " - " ASN E 532 " " NAG E 804 " - " ASN E 423 " " NAG F 1 " - " ASN E 540 " " NAG G 1 " - " ASN E 448 " " NAG I 1 " - " ASN E 623 " " NAG J 1 " - " ASN E 645 " " NAG K 1 " - " ASN E 556 " " NAG M 1 " - " ASN A 305 " " NAG N 1 " - " ASN A 196 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 31 sheets defined 8.0% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'E' and resid 438 through 443 removed outlier: 4.023A pdb=" N PHE E 442 " --> pdb=" O LEU E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 451 through 456 Processing helix chain 'E' and resid 593 through 598 Processing helix chain 'E' and resid 613 through 618 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.768A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.199A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.678A pdb=" N ASN B 31 " --> pdb=" O VAL B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.157A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 182 through 188 removed outlier: 3.610A pdb=" N HIS B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.595A pdb=" N GLY C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 497 through 498 Processing sheet with id=AA2, first strand: chain 'E' and resid 503 through 509 removed outlier: 4.551A pdb=" N MET E 555 " --> pdb=" O CYS E 503 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N THR E 553 " --> pdb=" O PRO E 505 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N TYR E 507 " --> pdb=" O GLY E 551 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLY E 551 " --> pdb=" O TYR E 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 607 through 608 removed outlier: 3.535A pdb=" N THR E 625 " --> pdb=" O CYS E 644 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 629 through 630 Processing sheet with id=AA5, first strand: chain 'E' and resid 658 through 659 removed outlier: 5.809A pdb=" N ASP E 658 " --> pdb=" O PHE E 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 671 through 673 removed outlier: 3.659A pdb=" N GLN E 700 " --> pdb=" O TRP E 672 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N HIS E 691 " --> pdb=" O TYR E 701 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.571A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.563A pdb=" N LYS H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN H 39 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.563A pdb=" N LYS H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N CYS H 92 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG H 94 " --> pdb=" O VAL H 100J" (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.703A pdb=" N LYS H 143 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER H 180 " --> pdb=" O CYS H 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.703A pdb=" N LYS H 143 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LYS H 143 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU H 178 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL H 169 " --> pdb=" O SER H 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 150 through 154 removed outlier: 3.548A pdb=" N SER H 153 " --> pdb=" O ASN H 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.593A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 11.946A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.034A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.139A pdb=" N GLN L 27 " --> pdb=" O GLU L 70 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLU L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY L 68 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.700A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.700A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 116 through 118 removed outlier: 3.692A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 153 through 155 removed outlier: 3.743A pdb=" N GLN L 155 " --> pdb=" O TRP L 148 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.818A pdb=" N HIS A 202 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 197 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 220 through 221 removed outlier: 3.707A pdb=" N ILE A 220 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 229 through 232 removed outlier: 4.309A pdb=" N VAL A 230 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG A 237 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 5 through 7 removed outlier: 4.176A pdb=" N SER B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS B 23 " --> pdb=" O PHE B 71 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE B 71 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.608A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.524A pdb=" N SER B 114 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN B 137 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR B 172 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 144 through 149 removed outlier: 3.766A pdb=" N VAL B 204 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 6 through 6A Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.707A pdb=" N GLU C 10 " --> pdb=" O ILE C 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 46 through 50 removed outlier: 6.871A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 70 through 72 removed outlier: 3.523A pdb=" N SER C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.826A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.826A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 175 " --> pdb=" O GLN C 171 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.742A pdb=" N THR C 151 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR C 194 " --> pdb=" O VAL C 211 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3121 1.35 - 1.47: 2624 1.47 - 1.59: 4291 1.59 - 1.71: 0 1.71 - 1.83: 60 Bond restraints: 10096 Sorted by residual: bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LEU B 2 " pdb=" CA LEU B 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N GLN C 3 " pdb=" CA GLN C 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N HIS E 421 " pdb=" CA HIS E 421 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 10091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 13212 1.54 - 3.07: 447 3.07 - 4.61: 92 4.61 - 6.14: 22 6.14 - 7.68: 6 Bond angle restraints: 13779 Sorted by residual: angle pdb=" C SER C 156 " pdb=" CA SER C 156 " pdb=" CB SER C 156 " ideal model delta sigma weight residual 116.54 110.82 5.72 1.15e+00 7.56e-01 2.47e+01 angle pdb=" N GLY C 100O" pdb=" CA GLY C 100O" pdb=" C GLY C 100O" ideal model delta sigma weight residual 113.18 120.86 -7.68 2.37e+00 1.78e-01 1.05e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.17 110.48 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" CA LEU E 689 " pdb=" C LEU E 689 " pdb=" O LEU E 689 " ideal model delta sigma weight residual 121.50 117.91 3.59 1.25e+00 6.40e-01 8.25e+00 angle pdb=" CA SER C 156 " pdb=" C SER C 156 " pdb=" N GLY C 157 " ideal model delta sigma weight residual 119.52 117.31 2.21 7.90e-01 1.60e+00 7.81e+00 ... (remaining 13774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 5867 21.62 - 43.24: 379 43.24 - 64.85: 60 64.85 - 86.47: 48 86.47 - 108.09: 26 Dihedral angle restraints: 6380 sinusoidal: 2769 harmonic: 3611 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual -86.00 -172.67 86.67 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual -86.00 -169.95 83.95 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CB CYS E 429 " pdb=" SG CYS E 429 " pdb=" SG CYS E 503 " pdb=" CB CYS E 503 " ideal model delta sinusoidal sigma weight residual 93.00 23.51 69.49 1 1.00e+01 1.00e-02 6.24e+01 ... (remaining 6377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1357 0.055 - 0.110: 213 0.110 - 0.165: 55 0.165 - 0.220: 2 0.220 - 0.275: 7 Chirality restraints: 1634 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1631 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 52I" 0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO C 52J" -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 52J" 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 52J" 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 646 " 0.013 2.00e-02 2.50e+03 1.57e-02 6.20e+00 pdb=" CG TRP E 646 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP E 646 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP E 646 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 646 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 646 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 646 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 646 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 646 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP E 646 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 148 " -0.039 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO H 149 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO H 149 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 149 " -0.029 5.00e-02 4.00e+02 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 107 2.56 - 3.14: 8370 3.14 - 3.73: 14219 3.73 - 4.31: 19492 4.31 - 4.90: 32530 Nonbonded interactions: 74718 Sorted by model distance: nonbonded pdb=" O ALA A 251 " pdb=" OG1 THR A 255 " model vdw 1.974 3.040 nonbonded pdb=" OD1 ASP A 233 " pdb=" OG SER A 235 " model vdw 2.021 3.040 nonbonded pdb=" O TYR B 185 " pdb=" OH TYR B 191 " model vdw 2.037 3.040 nonbonded pdb=" NE2 GLN C 192 " pdb=" O THR C 193 " model vdw 2.047 3.120 nonbonded pdb=" NH2 ARG L 61 " pdb=" O SER L 77 " model vdw 2.064 3.120 ... (remaining 74713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.590 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.004 0.034 10096 Z= 0.267 Angle : 0.688 7.679 13779 Z= 0.345 Chirality : 0.049 0.275 1634 Planarity : 0.005 0.079 1732 Dihedral : 16.992 108.091 4009 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1241 helix: -0.85 (0.82), residues: 48 sheet: -0.05 (0.26), residues: 426 loop : -1.20 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 646 HIS 0.006 0.001 HIS C 95 PHE 0.007 0.001 PHE H 146 TYR 0.021 0.001 TYR C 52I ARG 0.020 0.001 ARG E 543 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 431 ASP cc_start: 0.7749 (t0) cc_final: 0.7415 (t0) REVERT: E 546 GLN cc_start: 0.7942 (pp30) cc_final: 0.7291 (pp30) REVERT: H 91 TYR cc_start: 0.7205 (m-80) cc_final: 0.6275 (m-10) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2404 time to fit residues: 51.6945 Evaluate side-chains 116 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 467 GLN H 31 ASN H 55 ASN B 89 GLN B 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10096 Z= 0.275 Angle : 0.711 9.077 13779 Z= 0.361 Chirality : 0.047 0.193 1634 Planarity : 0.005 0.063 1732 Dihedral : 11.919 69.991 1927 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.24 % Allowed : 7.44 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.24), residues: 1241 helix: -1.36 (0.73), residues: 50 sheet: 0.03 (0.26), residues: 428 loop : -1.14 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 646 HIS 0.005 0.001 HIS E 589 PHE 0.021 0.002 PHE L 139 TYR 0.016 0.002 TYR C 194 ARG 0.005 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7993 (pp30) cc_final: 0.7357 (pp30) REVERT: E 656 ASP cc_start: 0.7715 (t0) cc_final: 0.7474 (t0) REVERT: H 91 TYR cc_start: 0.7223 (m-80) cc_final: 0.7002 (m-80) REVERT: H 206 LYS cc_start: 0.5318 (mmtt) cc_final: 0.5100 (mmtm) REVERT: A 309 TYR cc_start: 0.5465 (p90) cc_final: 0.4969 (p90) REVERT: B 89 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8111 (tm130) outliers start: 13 outliers final: 7 residues processed: 139 average time/residue: 0.2320 time to fit residues: 45.0793 Evaluate side-chains 124 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 38 optimal weight: 0.0170 chunk 90 optimal weight: 6.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10096 Z= 0.313 Angle : 0.699 10.101 13779 Z= 0.352 Chirality : 0.049 0.290 1634 Planarity : 0.005 0.058 1732 Dihedral : 7.954 54.730 1927 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.10 % Allowed : 11.15 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.29 (0.24), residues: 1241 helix: -1.48 (0.71), residues: 50 sheet: -0.16 (0.25), residues: 438 loop : -1.26 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 646 HIS 0.004 0.001 HIS E 589 PHE 0.021 0.002 PHE E 509 TYR 0.020 0.002 TYR B 91 ARG 0.004 0.001 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7953 (pp30) cc_final: 0.7392 (pp30) REVERT: E 610 ASP cc_start: 0.7909 (t0) cc_final: 0.7417 (t70) REVERT: H 206 LYS cc_start: 0.5463 (mmtt) cc_final: 0.5253 (mmtm) REVERT: L 139 PHE cc_start: 0.6803 (p90) cc_final: 0.6376 (p90) REVERT: B 139 PHE cc_start: 0.6287 (p90) cc_final: 0.5985 (p90) outliers start: 22 outliers final: 13 residues processed: 147 average time/residue: 0.2402 time to fit residues: 48.9661 Evaluate side-chains 136 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 699 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 0.0980 chunk 113 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10096 Z= 0.193 Angle : 0.639 9.126 13779 Z= 0.320 Chirality : 0.045 0.219 1634 Planarity : 0.005 0.057 1732 Dihedral : 6.108 59.801 1927 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.81 % Allowed : 12.68 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.24), residues: 1241 helix: -1.58 (0.68), residues: 50 sheet: 0.01 (0.25), residues: 423 loop : -1.16 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 646 HIS 0.002 0.001 HIS E 589 PHE 0.011 0.001 PHE E 509 TYR 0.015 0.001 TYR C 194 ARG 0.006 0.001 ARG E 630 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7888 (pp30) cc_final: 0.7321 (pp30) REVERT: E 610 ASP cc_start: 0.7769 (t0) cc_final: 0.7371 (t70) REVERT: E 644 CYS cc_start: 0.6867 (t) cc_final: 0.6479 (t) REVERT: E 656 ASP cc_start: 0.7684 (t0) cc_final: 0.7444 (t0) REVERT: H 91 TYR cc_start: 0.7495 (m-80) cc_final: 0.7006 (m-80) REVERT: H 206 LYS cc_start: 0.5377 (mmtt) cc_final: 0.5173 (mmtm) REVERT: A 219 MET cc_start: 0.7128 (tpp) cc_final: 0.6469 (ppp) REVERT: B 185 TYR cc_start: 0.5841 (t80) cc_final: 0.5011 (t80) REVERT: B 191 TYR cc_start: 0.3685 (m-80) cc_final: 0.2995 (m-80) REVERT: C 194 TYR cc_start: 0.3369 (OUTLIER) cc_final: 0.2119 (m-80) outliers start: 19 outliers final: 15 residues processed: 143 average time/residue: 0.2309 time to fit residues: 46.2347 Evaluate side-chains 140 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 194 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 0.1980 chunk 107 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 467 GLN ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 HIS ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10096 Z= 0.255 Angle : 0.639 9.625 13779 Z= 0.322 Chirality : 0.045 0.172 1634 Planarity : 0.005 0.057 1732 Dihedral : 5.615 57.927 1927 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.57 % Allowed : 14.39 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.24), residues: 1241 helix: -1.41 (0.71), residues: 50 sheet: -0.11 (0.25), residues: 431 loop : -1.21 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 646 HIS 0.003 0.001 HIS C 95 PHE 0.016 0.002 PHE E 509 TYR 0.016 0.001 TYR B 91 ARG 0.004 0.000 ARG E 630 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7909 (pp30) cc_final: 0.7359 (pp30) REVERT: E 579 LEU cc_start: 0.6357 (tp) cc_final: 0.6008 (tp) REVERT: E 610 ASP cc_start: 0.7843 (t0) cc_final: 0.7395 (t70) REVERT: E 644 CYS cc_start: 0.6976 (t) cc_final: 0.6573 (t) REVERT: E 656 ASP cc_start: 0.7769 (t0) cc_final: 0.7547 (t0) REVERT: B 185 TYR cc_start: 0.5887 (t80) cc_final: 0.5090 (t80) REVERT: B 191 TYR cc_start: 0.3670 (m-80) cc_final: 0.3156 (m-80) REVERT: C 100 MET cc_start: 0.7863 (ttm) cc_final: 0.7545 (ttm) REVERT: C 142 VAL cc_start: 0.8060 (t) cc_final: 0.7793 (m) REVERT: C 194 TYR cc_start: 0.3331 (OUTLIER) cc_final: 0.2074 (m-80) outliers start: 27 outliers final: 18 residues processed: 148 average time/residue: 0.2000 time to fit residues: 43.1876 Evaluate side-chains 145 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 194 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 0.0040 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 0.2980 chunk 9 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10096 Z= 0.201 Angle : 0.613 9.208 13779 Z= 0.309 Chirality : 0.044 0.180 1634 Planarity : 0.004 0.058 1732 Dihedral : 5.348 59.283 1927 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.86 % Allowed : 15.25 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1241 helix: -1.50 (0.68), residues: 50 sheet: -0.02 (0.25), residues: 425 loop : -1.14 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 646 HIS 0.003 0.001 HIS E 589 PHE 0.016 0.001 PHE L 139 TYR 0.013 0.001 TYR C 194 ARG 0.005 0.000 ARG E 630 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7886 (pp30) cc_final: 0.7321 (pp30) REVERT: E 644 CYS cc_start: 0.6817 (t) cc_final: 0.6443 (t) REVERT: B 185 TYR cc_start: 0.5822 (t80) cc_final: 0.5006 (t80) REVERT: B 191 TYR cc_start: 0.3740 (m-80) cc_final: 0.3293 (m-80) REVERT: C 100 MET cc_start: 0.7834 (ttm) cc_final: 0.7484 (ttm) REVERT: C 194 TYR cc_start: 0.3387 (OUTLIER) cc_final: 0.2102 (m-80) outliers start: 30 outliers final: 22 residues processed: 155 average time/residue: 0.2054 time to fit residues: 46.4775 Evaluate side-chains 147 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 194 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.0370 chunk 13 optimal weight: 0.5980 chunk 68 optimal weight: 20.0000 chunk 87 optimal weight: 0.2980 chunk 67 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 chunk 119 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.0770 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 638 HIS ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN C 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10096 Z= 0.153 Angle : 0.599 9.692 13779 Z= 0.299 Chirality : 0.043 0.189 1634 Planarity : 0.004 0.059 1732 Dihedral : 4.901 55.224 1927 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.00 % Allowed : 17.06 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.23), residues: 1241 helix: -1.23 (0.71), residues: 50 sheet: -0.02 (0.24), residues: 442 loop : -0.98 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 646 HIS 0.002 0.000 HIS E 589 PHE 0.010 0.001 PHE B 118 TYR 0.011 0.001 TYR C 145 ARG 0.008 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7784 (pp30) cc_final: 0.7274 (pp30) REVERT: E 644 CYS cc_start: 0.6850 (t) cc_final: 0.6496 (t) REVERT: H 91 TYR cc_start: 0.7531 (m-80) cc_final: 0.7234 (m-80) REVERT: A 219 MET cc_start: 0.6866 (tpp) cc_final: 0.6397 (ppp) REVERT: B 185 TYR cc_start: 0.5930 (t80) cc_final: 0.5199 (t80) REVERT: B 191 TYR cc_start: 0.3724 (m-80) cc_final: 0.3337 (m-80) REVERT: C 66 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.6101 (tt0) outliers start: 21 outliers final: 17 residues processed: 148 average time/residue: 0.2219 time to fit residues: 46.7754 Evaluate side-chains 142 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 59 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10096 Z= 0.236 Angle : 0.628 8.800 13779 Z= 0.316 Chirality : 0.045 0.179 1634 Planarity : 0.005 0.056 1732 Dihedral : 5.117 59.223 1927 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.19 % Allowed : 17.16 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.24), residues: 1241 helix: -1.03 (0.74), residues: 50 sheet: -0.12 (0.24), residues: 443 loop : -1.06 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 646 HIS 0.003 0.001 HIS C 95 PHE 0.017 0.002 PHE L 139 TYR 0.015 0.001 TYR B 91 ARG 0.005 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7859 (pp30) cc_final: 0.7332 (pp30) REVERT: E 644 CYS cc_start: 0.6951 (t) cc_final: 0.6551 (t) REVERT: L 79 GLN cc_start: 0.7315 (mm-40) cc_final: 0.7087 (mp10) REVERT: A 219 MET cc_start: 0.6835 (tpp) cc_final: 0.6319 (ppp) REVERT: B 185 TYR cc_start: 0.5921 (t80) cc_final: 0.5165 (t80) REVERT: B 191 TYR cc_start: 0.3986 (m-80) cc_final: 0.3543 (m-80) REVERT: C 100 MET cc_start: 0.7872 (ttm) cc_final: 0.7591 (ttm) outliers start: 23 outliers final: 21 residues processed: 147 average time/residue: 0.2071 time to fit residues: 44.4454 Evaluate side-chains 149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 677 CYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 169 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 0.0570 chunk 67 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 87 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10096 Z= 0.178 Angle : 0.605 8.424 13779 Z= 0.302 Chirality : 0.044 0.181 1634 Planarity : 0.005 0.058 1732 Dihedral : 4.935 57.788 1927 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.38 % Allowed : 16.87 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.24), residues: 1241 helix: -1.00 (0.75), residues: 50 sheet: -0.08 (0.24), residues: 445 loop : -0.99 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 646 HIS 0.002 0.000 HIS E 589 PHE 0.010 0.001 PHE E 509 TYR 0.009 0.001 TYR C 145 ARG 0.006 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 644 CYS cc_start: 0.6875 (t) cc_final: 0.6497 (t) REVERT: H 91 TYR cc_start: 0.7664 (m-80) cc_final: 0.7371 (m-80) REVERT: L 110 VAL cc_start: 0.8434 (m) cc_final: 0.8224 (p) REVERT: A 219 MET cc_start: 0.6872 (tpp) cc_final: 0.6411 (ppp) REVERT: B 122 ASP cc_start: 0.7422 (m-30) cc_final: 0.7144 (m-30) REVERT: B 185 TYR cc_start: 0.5939 (t80) cc_final: 0.5235 (t80) REVERT: B 191 TYR cc_start: 0.3900 (m-80) cc_final: 0.3535 (m-80) REVERT: C 66 GLN cc_start: 0.6624 (OUTLIER) cc_final: 0.6104 (tt0) outliers start: 25 outliers final: 21 residues processed: 148 average time/residue: 0.2200 time to fit residues: 46.6442 Evaluate side-chains 149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 636 VAL Chi-restraints excluded: chain E residue 677 CYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 10 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10096 Z= 0.269 Angle : 0.647 8.937 13779 Z= 0.324 Chirality : 0.045 0.169 1634 Planarity : 0.005 0.054 1732 Dihedral : 5.194 59.874 1927 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.48 % Allowed : 17.06 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.24), residues: 1241 helix: -0.92 (0.77), residues: 50 sheet: -0.15 (0.24), residues: 441 loop : -1.05 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP E 646 HIS 0.005 0.001 HIS C 95 PHE 0.017 0.002 PHE L 139 TYR 0.018 0.001 TYR B 91 ARG 0.005 0.000 ARG C 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 644 CYS cc_start: 0.6922 (t) cc_final: 0.6556 (t) REVERT: L 108 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7608 (ttp80) REVERT: L 110 VAL cc_start: 0.8459 (m) cc_final: 0.8252 (p) REVERT: A 219 MET cc_start: 0.6939 (tpp) cc_final: 0.6414 (ppp) REVERT: B 185 TYR cc_start: 0.5959 (t80) cc_final: 0.5191 (t80) REVERT: B 191 TYR cc_start: 0.4103 (m-80) cc_final: 0.3653 (m-80) REVERT: C 66 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.6268 (tt0) REVERT: C 100 MET cc_start: 0.7859 (ttm) cc_final: 0.7602 (ttm) outliers start: 26 outliers final: 23 residues processed: 145 average time/residue: 0.1970 time to fit residues: 41.8099 Evaluate side-chains 148 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 636 VAL Chi-restraints excluded: chain E residue 677 CYS Chi-restraints excluded: chain E residue 698 ASP Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.210028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163135 restraints weight = 13874.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.156730 restraints weight = 17969.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.160117 restraints weight = 18678.689| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10096 Z= 0.214 Angle : 0.640 9.375 13779 Z= 0.320 Chirality : 0.045 0.184 1634 Planarity : 0.005 0.057 1732 Dihedral : 5.150 59.577 1927 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.57 % Allowed : 17.16 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.24), residues: 1241 helix: -1.11 (0.73), residues: 50 sheet: -0.15 (0.24), residues: 439 loop : -1.04 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP E 646 HIS 0.004 0.001 HIS C 95 PHE 0.013 0.001 PHE E 509 TYR 0.013 0.001 TYR B 91 ARG 0.006 0.000 ARG C 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.36 seconds wall clock time: 40 minutes 18.55 seconds (2418.55 seconds total)