Starting phenix.real_space_refine on Thu Jul 2 19:43:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fsj_29419/07_2026/8fsj_29419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fsj_29419/07_2026/8fsj_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fsj_29419/07_2026/8fsj_29419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fsj_29419/07_2026/8fsj_29419.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fsj_29419/07_2026/8fsj_29419.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fsj_29419/07_2026/8fsj_29419.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fsj_29419/07_2026/8fsj_29419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fsj_29419/07_2026/8fsj_29419.map" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS: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: {'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1} 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, 'TRP:plan': 1, 'ASN:plan1': 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 1.55, per 1000 atoms: 0.16 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: 1.04 Conformation dependent library (CDL) restraints added in 370.5 milliseconds 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: 0.32 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: 1.57 Time building geometry restraints manager: 1.32 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 - 17.90: 5283 17.90 - 35.80: 421 35.80 - 53.70: 75 53.70 - 71.61: 15 71.61 - 89.51: 10 Dihedral angle restraints: 5804 sinusoidal: 2193 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 5801 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: 3.830 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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 10145 Z= 0.194 Angle : 0.701 7.679 13905 Z= 0.349 Chirality : 0.049 0.275 1634 Planarity : 0.005 0.079 1732 Dihedral : 13.162 89.507 3433 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.77 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (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 ARG 0.020 0.001 ARG E 543 TYR 0.021 0.001 TYR C 52I PHE 0.007 0.001 PHE H 146 TRP 0.040 0.002 TRP E 646 HIS 0.006 0.001 HIS C 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (10096) covalent geometry : angle 0.68837 / 0.35 (13779) SS BOND : bond 0.00471 / 0.32 ( 21) SS BOND : angle 1.51281 / 1.11 ( 42) hydrogen bonds : bond 0.27125 / 18.66 ( 244) hydrogen bonds : angle 11.09980 / 7.76 ( 657) link_BETA1-4 : bond 0.00341 / 0.24 ( 14) link_BETA1-4 : angle 1.22524 / 0.92 ( 42) link_NAG-ASN : bond 0.00381 / 0.28 ( 14) link_NAG-ASN : angle 1.85349 / 1.41 ( 42) *********************** 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 : 0.360 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: 0.1033 time to fit residues: 22.4157 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 : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 31 ASN H 55 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.206598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.165475 restraints weight = 13901.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.164167 restraints weight = 23948.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.166108 restraints weight = 18944.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.166002 restraints weight = 12281.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.169495 restraints weight = 10068.780| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10145 Z= 0.211 Angle : 0.729 9.615 13905 Z= 0.371 Chirality : 0.047 0.190 1634 Planarity : 0.005 0.063 1732 Dihedral : 4.875 30.353 1351 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.24 % Allowed : 8.77 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.24), residues: 1241 helix: -1.45 (0.71), residues: 50 sheet: -0.06 (0.26), residues: 428 loop : -1.19 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 38 TYR 0.021 0.002 TYR C 194 PHE 0.021 0.002 PHE L 139 TRP 0.032 0.002 TRP E 646 HIS 0.006 0.001 HIS E 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (10096) covalent geometry : angle 0.71566 / 0.37 (13779) SS BOND : bond 0.00462 / 0.33 ( 21) SS BOND : angle 1.35827 / 0.94 ( 42) hydrogen bonds : bond 0.04973 / 3.30 ( 244) hydrogen bonds : angle 8.00160 / 5.58 ( 657) link_BETA1-4 : bond 0.00400 / 0.27 ( 14) link_BETA1-4 : angle 1.41971 / 1.02 ( 42) link_NAG-ASN : bond 0.00449 / 0.30 ( 14) link_NAG-ASN : angle 2.05149 / 1.55 ( 42) *********************** 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 142 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 431 ASP cc_start: 0.7983 (t0) cc_final: 0.7691 (t0) REVERT: E 546 GLN cc_start: 0.7971 (pp30) cc_final: 0.7334 (pp30) REVERT: E 579 LEU cc_start: 0.5853 (tp) cc_final: 0.5628 (tp) REVERT: A 309 TYR cc_start: 0.5427 (p90) cc_final: 0.4857 (p90) outliers start: 13 outliers final: 8 residues processed: 137 average time/residue: 0.1131 time to fit residues: 21.6700 Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 L residue 65 SER 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 118 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 0.3980 chunk 86 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.206066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.159627 restraints weight = 13592.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.152326 restraints weight = 16591.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.155768 restraints weight = 17137.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155863 restraints weight = 10375.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.158961 restraints weight = 9060.977| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10145 Z= 0.151 Angle : 0.653 9.561 13905 Z= 0.329 Chirality : 0.045 0.162 1634 Planarity : 0.005 0.058 1732 Dihedral : 4.730 28.246 1351 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.53 % Allowed : 12.01 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.24), residues: 1241 helix: -1.51 (0.72), residues: 50 sheet: -0.05 (0.25), residues: 423 loop : -1.17 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 94 TYR 0.015 0.001 TYR B 191 PHE 0.015 0.002 PHE E 509 TRP 0.025 0.002 TRP E 646 HIS 0.003 0.001 HIS H 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (10096) covalent geometry : angle 0.64041 / 0.33 (13779) SS BOND : bond 0.00353 / 0.26 ( 21) SS BOND : angle 1.07620 / 0.76 ( 42) hydrogen bonds : bond 0.03709 / 2.48 ( 244) hydrogen bonds : angle 7.04172 / 4.92 ( 657) link_BETA1-4 : bond 0.00419 / 0.30 ( 14) link_BETA1-4 : angle 1.32866 / 0.96 ( 42) link_NAG-ASN : bond 0.00363 / 0.26 ( 14) link_NAG-ASN : angle 1.93297 / 1.45 ( 42) *********************** 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 151 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 431 ASP cc_start: 0.7993 (t0) cc_final: 0.7696 (t0) REVERT: E 546 GLN cc_start: 0.7995 (pp30) cc_final: 0.7357 (pp30) REVERT: E 610 ASP cc_start: 0.7973 (t0) cc_final: 0.7511 (t70) REVERT: E 656 ASP cc_start: 0.7771 (t0) cc_final: 0.7537 (t0) REVERT: H 91 TYR cc_start: 0.7078 (m-80) cc_final: 0.6854 (m-80) REVERT: L 139 PHE cc_start: 0.7036 (p90) cc_final: 0.6567 (p90) REVERT: B 123 GLU cc_start: 0.8609 (tp30) cc_final: 0.8377 (mp0) REVERT: B 185 TYR cc_start: 0.6152 (t80) cc_final: 0.5479 (t80) REVERT: B 191 TYR cc_start: 0.4054 (m-80) cc_final: 0.3185 (m-80) outliers start: 16 outliers final: 9 residues processed: 143 average time/residue: 0.1051 time to fit residues: 21.1339 Evaluate side-chains 131 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 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 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 47 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 55 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.205999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.162231 restraints weight = 13961.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.159729 restraints weight = 22158.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.161422 restraints weight = 20780.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.162765 restraints weight = 11546.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.163916 restraints weight = 9532.348| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10145 Z= 0.157 Angle : 0.659 9.550 13905 Z= 0.329 Chirality : 0.045 0.208 1634 Planarity : 0.005 0.056 1732 Dihedral : 4.702 29.078 1351 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.29 % Allowed : 13.82 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.24), residues: 1241 helix: -1.49 (0.72), residues: 50 sheet: -0.10 (0.25), residues: 431 loop : -1.19 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 630 TYR 0.014 0.001 TYR A 201 PHE 0.016 0.002 PHE E 509 TRP 0.039 0.002 TRP E 646 HIS 0.003 0.001 HIS E 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (10096) covalent geometry : angle 0.64748 / 0.33 (13779) SS BOND : bond 0.00408 / 0.29 ( 21) SS BOND : angle 1.03989 / 0.73 ( 42) hydrogen bonds : bond 0.03259 / 2.19 ( 244) hydrogen bonds : angle 6.76285 / 4.74 ( 657) link_BETA1-4 : bond 0.00383 / 0.28 ( 14) link_BETA1-4 : angle 1.27740 / 0.93 ( 42) link_NAG-ASN : bond 0.00359 / 0.25 ( 14) link_NAG-ASN : angle 1.86560 / 1.41 ( 42) *********************** 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 151 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 431 ASP cc_start: 0.7965 (t0) cc_final: 0.7709 (t0) REVERT: E 546 GLN cc_start: 0.7917 (pp30) cc_final: 0.7345 (pp30) REVERT: E 563 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8018 (m) REVERT: E 610 ASP cc_start: 0.7984 (t0) cc_final: 0.7553 (t70) REVERT: E 644 CYS cc_start: 0.6806 (t) cc_final: 0.6403 (t) REVERT: E 656 ASP cc_start: 0.7828 (t0) cc_final: 0.7589 (t0) REVERT: C 142 VAL cc_start: 0.8092 (t) cc_final: 0.7833 (m) outliers start: 24 outliers final: 18 residues processed: 145 average time/residue: 0.0984 time to fit residues: 20.4410 Evaluate side-chains 140 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 607 CYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 75 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 55 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.205758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160341 restraints weight = 13698.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.160507 restraints weight = 21939.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.162320 restraints weight = 16719.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.162974 restraints weight = 10091.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.164508 restraints weight = 8615.701| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10145 Z= 0.140 Angle : 0.637 9.463 13905 Z= 0.317 Chirality : 0.044 0.169 1634 Planarity : 0.005 0.059 1732 Dihedral : 4.596 27.480 1351 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.38 % Allowed : 15.16 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.24), residues: 1241 helix: -1.56 (0.69), residues: 50 sheet: -0.02 (0.25), residues: 424 loop : -1.20 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.012 0.001 TYR A 201 PHE 0.013 0.001 PHE E 509 TRP 0.026 0.001 TRP E 646 HIS 0.003 0.001 HIS E 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (10096) covalent geometry : angle 0.62514 / 0.31 (13779) SS BOND : bond 0.00341 / 0.25 ( 21) SS BOND : angle 1.08632 / 0.74 ( 42) hydrogen bonds : bond 0.03146 / 2.14 ( 244) hydrogen bonds : angle 6.51358 / 4.55 ( 657) link_BETA1-4 : bond 0.00392 / 0.29 ( 14) link_BETA1-4 : angle 1.23587 / 0.90 ( 42) link_NAG-ASN : bond 0.00345 / 0.24 ( 14) link_NAG-ASN : angle 1.81197 / 1.36 ( 42) *********************** 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 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 431 ASP cc_start: 0.8030 (t0) cc_final: 0.7741 (t0) REVERT: E 546 GLN cc_start: 0.7918 (pp30) cc_final: 0.7350 (pp30) REVERT: E 563 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.8038 (m) REVERT: E 610 ASP cc_start: 0.7953 (t0) cc_final: 0.7553 (t70) REVERT: E 644 CYS cc_start: 0.6683 (t) cc_final: 0.6278 (t) REVERT: E 656 ASP cc_start: 0.7786 (t0) cc_final: 0.7547 (t0) REVERT: A 219 MET cc_start: 0.6725 (tpp) cc_final: 0.6282 (ppp) REVERT: B 4 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7856 (mm) REVERT: B 122 ASP cc_start: 0.7373 (m-30) cc_final: 0.7115 (m-30) REVERT: B 191 TYR cc_start: 0.3215 (m-80) cc_final: 0.2987 (m-80) outliers start: 25 outliers final: 17 residues processed: 149 average time/residue: 0.0913 time to fit residues: 20.0593 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 : 0.390 ------------------------------------------------------------------------------- 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 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 65 SER Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 4 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 76 optimal weight: 0.0270 chunk 22 optimal weight: 0.6980 chunk 101 optimal weight: 0.0670 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 589 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.208457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.162127 restraints weight = 13833.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.154064 restraints weight = 16218.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.156910 restraints weight = 18376.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.157307 restraints weight = 10901.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.161356 restraints weight = 9074.602| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10145 Z= 0.111 Angle : 0.599 8.737 13905 Z= 0.299 Chirality : 0.043 0.168 1634 Planarity : 0.005 0.058 1732 Dihedral : 4.415 24.168 1351 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.10 % Allowed : 16.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.23), residues: 1241 helix: -1.35 (0.72), residues: 50 sheet: 0.05 (0.25), residues: 425 loop : -1.10 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 94 TYR 0.010 0.001 TYR C 145 PHE 0.017 0.001 PHE L 139 TRP 0.043 0.002 TRP E 646 HIS 0.002 0.001 HIS E 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (10096) covalent geometry : angle 0.58944 / 0.30 (13779) SS BOND : bond 0.00302 / 0.21 ( 21) SS BOND : angle 0.84851 / 0.60 ( 42) hydrogen bonds : bond 0.02790 / 1.90 ( 244) hydrogen bonds : angle 6.18933 / 4.31 ( 657) link_BETA1-4 : bond 0.00405 / 0.30 ( 14) link_BETA1-4 : angle 1.18116 / 0.85 ( 42) link_NAG-ASN : bond 0.00320 / 0.23 ( 14) link_NAG-ASN : angle 1.61096 / 1.19 ( 42) *********************** 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 158 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7860 (pp30) cc_final: 0.7293 (pp30) REVERT: E 644 CYS cc_start: 0.6767 (t) cc_final: 0.6426 (t) REVERT: L 38 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8175 (tm-30) REVERT: A 219 MET cc_start: 0.7294 (tpp) cc_final: 0.6334 (ppp) REVERT: B 96 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.8008 (pt) REVERT: B 105 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6869 (mt-10) REVERT: B 123 GLU cc_start: 0.8590 (tp30) cc_final: 0.8359 (mp0) outliers start: 22 outliers final: 16 residues processed: 152 average time/residue: 0.0907 time to fit residues: 20.2692 Evaluate side-chains 143 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 42 optimal weight: 40.0000 chunk 49 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 79 optimal weight: 0.0270 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 200 HIS ** 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 = 0.4478 r_free = 0.4478 target = 0.207241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.162149 restraints weight = 13722.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.163763 restraints weight = 21240.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.164628 restraints weight = 16029.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.164635 restraints weight = 10729.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.167454 restraints weight = 8686.015| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10145 Z= 0.134 Angle : 0.619 8.975 13905 Z= 0.308 Chirality : 0.044 0.159 1634 Planarity : 0.004 0.057 1732 Dihedral : 4.432 26.060 1351 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.57 % Allowed : 16.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.23), residues: 1241 helix: -1.25 (0.72), residues: 50 sheet: -0.08 (0.25), residues: 441 loop : -1.10 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 630 TYR 0.012 0.001 TYR B 91 PHE 0.012 0.002 PHE B 139 TRP 0.037 0.002 TRP E 646 HIS 0.002 0.001 HIS C 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 (10096) covalent geometry : angle 0.60958 / 0.31 (13779) SS BOND : bond 0.00323 / 0.23 ( 21) SS BOND : angle 0.92620 / 0.64 ( 42) hydrogen bonds : bond 0.02813 / 1.94 ( 244) hydrogen bonds : angle 6.07549 / 4.23 ( 657) link_BETA1-4 : bond 0.00395 / 0.29 ( 14) link_BETA1-4 : angle 1.18868 / 0.86 ( 42) link_NAG-ASN : bond 0.00342 / 0.24 ( 14) link_NAG-ASN : angle 1.60329 / 1.20 ( 42) *********************** 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 153 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 431 ASP cc_start: 0.7889 (t0) cc_final: 0.7652 (t0) REVERT: E 546 GLN cc_start: 0.7885 (pp30) cc_final: 0.7332 (pp30) REVERT: E 644 CYS cc_start: 0.6680 (t) cc_final: 0.6298 (t) REVERT: L 79 GLN cc_start: 0.7374 (mm-40) cc_final: 0.7124 (mp10) REVERT: A 219 MET cc_start: 0.7027 (tpp) cc_final: 0.6447 (ppp) REVERT: B 96 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8015 (pt) REVERT: C 66 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6196 (tt0) outliers start: 27 outliers final: 20 residues processed: 148 average time/residue: 0.0891 time to fit residues: 19.4772 Evaluate side-chains 146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 608 LEU Chi-restraints excluded: chain E residue 636 VAL 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 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 96 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 123 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.208603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.165297 restraints weight = 13691.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.167351 restraints weight = 23305.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.168290 restraints weight = 14728.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.169278 restraints weight = 9460.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.169856 restraints weight = 8427.736| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10145 Z= 0.154 Angle : 0.634 9.194 13905 Z= 0.317 Chirality : 0.045 0.171 1634 Planarity : 0.005 0.056 1732 Dihedral : 4.494 27.377 1351 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.96 % Allowed : 16.97 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1241 helix: -1.20 (0.72), residues: 50 sheet: -0.12 (0.24), residues: 440 loop : -1.12 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 630 TYR 0.014 0.001 TYR B 91 PHE 0.018 0.002 PHE L 139 TRP 0.034 0.002 TRP E 646 HIS 0.003 0.001 HIS C 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (10096) covalent geometry : angle 0.62344 / 0.32 (13779) SS BOND : bond 0.00353 / 0.25 ( 21) SS BOND : angle 1.09073 / 0.73 ( 42) hydrogen bonds : bond 0.02850 / 1.97 ( 244) hydrogen bonds : angle 6.00961 / 4.19 ( 657) link_BETA1-4 : bond 0.00392 / 0.28 ( 14) link_BETA1-4 : angle 1.19352 / 0.87 ( 42) link_NAG-ASN : bond 0.00346 / 0.24 ( 14) link_NAG-ASN : angle 1.66755 / 1.25 ( 42) *********************** 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 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7885 (pp30) cc_final: 0.7323 (pp30) REVERT: E 563 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8058 (m) REVERT: E 644 CYS cc_start: 0.6826 (t) cc_final: 0.6451 (t) REVERT: A 219 MET cc_start: 0.7048 (tpp) cc_final: 0.6464 (ppp) REVERT: B 4 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7794 (mm) REVERT: B 96 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8034 (pt) REVERT: B 122 ASP cc_start: 0.7290 (m-30) cc_final: 0.7057 (m-30) REVERT: B 191 TYR cc_start: 0.2417 (m-80) cc_final: 0.2133 (m-10) REVERT: C 100 MET cc_start: 0.7841 (ttm) cc_final: 0.7546 (ttm) outliers start: 31 outliers final: 25 residues processed: 149 average time/residue: 0.0889 time to fit residues: 19.7971 Evaluate side-chains 149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 E residue 629 VAL Chi-restraints excluded: chain E residue 636 VAL Chi-restraints excluded: chain E residue 677 CYS Chi-restraints excluded: chain E residue 699 VAL 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 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 4 LEU 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 46 GLU 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 63 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 0.0570 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 200 HIS ** 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 = 0.4488 r_free = 0.4488 target = 0.210433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.167858 restraints weight = 13762.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.171397 restraints weight = 22331.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.171918 restraints weight = 12582.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.172481 restraints weight = 8661.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.173201 restraints weight = 7820.930| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10145 Z= 0.123 Angle : 0.618 8.793 13905 Z= 0.309 Chirality : 0.044 0.211 1634 Planarity : 0.005 0.059 1732 Dihedral : 4.391 24.946 1351 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.96 % Allowed : 17.06 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.24), residues: 1241 helix: -1.12 (0.74), residues: 50 sheet: -0.06 (0.25), residues: 440 loop : -1.08 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 630 TYR 0.014 0.001 TYR B 191 PHE 0.013 0.001 PHE L 118 TRP 0.032 0.001 TRP E 646 HIS 0.003 0.001 HIS C 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (10096) covalent geometry : angle 0.60909 / 0.31 (13779) SS BOND : bond 0.00295 / 0.21 ( 21) SS BOND : angle 0.90097 / 0.63 ( 42) hydrogen bonds : bond 0.02680 / 1.87 ( 244) hydrogen bonds : angle 5.88193 / 4.09 ( 657) link_BETA1-4 : bond 0.00397 / 0.29 ( 14) link_BETA1-4 : angle 1.15047 / 0.83 ( 42) link_NAG-ASN : bond 0.00329 / 0.24 ( 14) link_NAG-ASN : angle 1.56530 / 1.16 ( 42) *********************** 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 158 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7794 (pp30) cc_final: 0.7259 (pp30) REVERT: E 644 CYS cc_start: 0.6689 (t) cc_final: 0.6337 (t) REVERT: A 219 MET cc_start: 0.7114 (tpp) cc_final: 0.6461 (ppp) REVERT: B 4 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7771 (mm) REVERT: B 96 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8013 (pt) REVERT: C 66 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.6079 (tt0) REVERT: C 100 MET cc_start: 0.7853 (ttm) cc_final: 0.7547 (ttm) outliers start: 31 outliers final: 24 residues processed: 150 average time/residue: 0.0938 time to fit residues: 20.6012 Evaluate side-chains 150 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 608 LEU Chi-restraints excluded: chain E residue 629 VAL 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 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 4 LEU Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 LEU 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 78 optimal weight: 2.9990 chunk 10 optimal weight: 0.0020 chunk 91 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.4966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4493 r_free = 0.4493 target = 0.210970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.168020 restraints weight = 13739.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.169357 restraints weight = 23222.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.170650 restraints weight = 16877.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.171267 restraints weight = 10411.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.172364 restraints weight = 9022.083| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10145 Z= 0.116 Angle : 0.625 8.874 13905 Z= 0.312 Chirality : 0.044 0.243 1634 Planarity : 0.005 0.058 1732 Dihedral : 4.343 24.183 1351 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.67 % Allowed : 17.16 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.24), residues: 1241 helix: -1.04 (0.75), residues: 50 sheet: -0.07 (0.24), residues: 441 loop : -1.04 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 630 TYR 0.018 0.001 TYR B 191 PHE 0.020 0.001 PHE L 139 TRP 0.031 0.001 TRP E 646 HIS 0.003 0.001 HIS C 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (10096) covalent geometry : angle 0.61695 / 0.31 (13779) SS BOND : bond 0.00289 / 0.20 ( 21) SS BOND : angle 0.89362 / 0.63 ( 42) hydrogen bonds : bond 0.02629 / 1.84 ( 244) hydrogen bonds : angle 5.81172 / 4.04 ( 657) link_BETA1-4 : bond 0.00406 / 0.30 ( 14) link_BETA1-4 : angle 1.14190 / 0.82 ( 42) link_NAG-ASN : bond 0.00320 / 0.23 ( 14) link_NAG-ASN : angle 1.52086 / 1.12 ( 42) ********************** 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 155 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 644 CYS cc_start: 0.6669 (t) cc_final: 0.6318 (t) REVERT: A 219 MET cc_start: 0.7119 (tpp) cc_final: 0.6456 (ppp) REVERT: B 96 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7997 (pt) REVERT: B 122 ASP cc_start: 0.7193 (m-30) cc_final: 0.6933 (m-30) REVERT: C 66 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.6196 (tt0) REVERT: C 100 MET cc_start: 0.7840 (ttm) cc_final: 0.7537 (ttm) outliers start: 28 outliers final: 25 residues processed: 147 average time/residue: 0.0949 time to fit residues: 20.3988 Evaluate side-chains 151 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 608 LEU Chi-restraints excluded: chain E residue 629 VAL 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 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 104 LEU 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 117 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.0050 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4485 r_free = 0.4485 target = 0.210166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.165932 restraints weight = 13708.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.164905 restraints weight = 22417.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.166777 restraints weight = 19041.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.167519 restraints weight = 11062.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.169492 restraints weight = 9238.662| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10145 Z= 0.117 Angle : 0.617 8.594 13905 Z= 0.306 Chirality : 0.044 0.163 1634 Planarity : 0.005 0.060 1732 Dihedral : 4.333 24.277 1351 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.76 % Allowed : 17.54 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.24), residues: 1241 helix: -1.04 (0.75), residues: 50 sheet: -0.03 (0.25), residues: 435 loop : -1.04 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 630 TYR 0.019 0.001 TYR B 191 PHE 0.014 0.001 PHE L 118 TRP 0.030 0.001 TRP E 646 HIS 0.003 0.001 HIS C 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10096) covalent geometry : angle 0.60897 / 0.30 (13779) SS BOND : bond 0.00302 / 0.22 ( 21) SS BOND : angle 0.88946 / 0.62 ( 42) hydrogen bonds : bond 0.02622 / 1.84 ( 244) hydrogen bonds : angle 5.75194 / 4.01 ( 657) link_BETA1-4 : bond 0.00403 / 0.30 ( 14) link_BETA1-4 : angle 1.14043 / 0.82 ( 42) link_NAG-ASN : bond 0.00319 / 0.23 ( 14) link_NAG-ASN : angle 1.50397 / 1.11 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1733.90 seconds wall clock time: 30 minutes 56.75 seconds (1856.75 seconds total)