Starting phenix.real_space_refine on Sat Aug 23 05:23:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fsj_29419/08_2025/8fsj_29419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fsj_29419/08_2025/8fsj_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_29419/08_2025/8fsj_29419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fsj_29419/08_2025/8fsj_29419.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fsj_29419/08_2025/8fsj_29419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fsj_29419/08_2025/8fsj_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.02, per 1000 atoms: 0.31 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: 1.25 Conformation dependent library (CDL) restraints added in 395.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.49 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: 1.94 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3121 1.35 - 1.47: 2624 1.47 - 1.59: 4291 1.59 - 1.71: 0 1.71 - 1.83: 60 Bond restraints: 10096 Sorted by residual: bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LEU B 2 " pdb=" CA LEU B 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N GLN C 3 " pdb=" CA GLN C 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N HIS E 421 " pdb=" CA HIS E 421 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 10091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 13212 1.54 - 3.07: 447 3.07 - 4.61: 92 4.61 - 6.14: 22 6.14 - 7.68: 6 Bond angle restraints: 13779 Sorted by residual: angle pdb=" C SER C 156 " pdb=" CA SER C 156 " pdb=" CB SER C 156 " ideal model delta sigma weight residual 116.54 110.82 5.72 1.15e+00 7.56e-01 2.47e+01 angle pdb=" N GLY C 100O" pdb=" CA GLY C 100O" pdb=" C GLY C 100O" ideal model delta sigma weight residual 113.18 120.86 -7.68 2.37e+00 1.78e-01 1.05e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.17 110.48 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" CA LEU E 689 " pdb=" C LEU E 689 " pdb=" O LEU E 689 " ideal model delta sigma weight residual 121.50 117.91 3.59 1.25e+00 6.40e-01 8.25e+00 angle pdb=" CA SER C 156 " pdb=" C SER C 156 " pdb=" N GLY C 157 " ideal model delta sigma weight residual 119.52 117.31 2.21 7.90e-01 1.60e+00 7.81e+00 ... (remaining 13774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 5867 21.62 - 43.24: 379 43.24 - 64.85: 60 64.85 - 86.47: 48 86.47 - 108.09: 26 Dihedral angle restraints: 6380 sinusoidal: 2769 harmonic: 3611 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual -86.00 -172.67 86.67 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual -86.00 -169.95 83.95 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CB CYS E 429 " pdb=" SG CYS E 429 " pdb=" SG CYS E 503 " pdb=" CB CYS E 503 " ideal model delta sinusoidal sigma weight residual 93.00 23.51 69.49 1 1.00e+01 1.00e-02 6.24e+01 ... (remaining 6377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1357 0.055 - 0.110: 213 0.110 - 0.165: 55 0.165 - 0.220: 2 0.220 - 0.275: 7 Chirality restraints: 1634 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1631 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 52I" 0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO C 52J" -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 52J" 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 52J" 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 646 " 0.013 2.00e-02 2.50e+03 1.57e-02 6.20e+00 pdb=" CG TRP E 646 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP E 646 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP E 646 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 646 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 646 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 646 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 646 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 646 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP E 646 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 148 " -0.039 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO H 149 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO H 149 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 149 " -0.029 5.00e-02 4.00e+02 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 107 2.56 - 3.14: 8370 3.14 - 3.73: 14219 3.73 - 4.31: 19492 4.31 - 4.90: 32530 Nonbonded interactions: 74718 Sorted by model distance: nonbonded pdb=" O ALA A 251 " pdb=" OG1 THR A 255 " model vdw 1.974 3.040 nonbonded pdb=" OD1 ASP A 233 " pdb=" OG SER A 235 " model vdw 2.021 3.040 nonbonded pdb=" O TYR B 185 " pdb=" OH TYR B 191 " model vdw 2.037 3.040 nonbonded pdb=" NE2 GLN C 192 " pdb=" O THR C 193 " model vdw 2.047 3.120 nonbonded pdb=" NH2 ARG L 61 " pdb=" O SER L 77 " model vdw 2.064 3.120 ... (remaining 74713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 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: 0.030 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 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 : 16.992 108.091 4009 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 aren 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 covalent geometry : bond 0.00409 (10096) covalent geometry : angle 0.68837 (13779) SS BOND : bond 0.00471 ( 21) SS BOND : angle 1.51281 ( 42) hydrogen bonds : bond 0.27125 ( 244) hydrogen bonds : angle 11.09980 ( 657) link_BETA1-4 : bond 0.00341 ( 14) link_BETA1-4 : angle 1.22524 ( 42) link_NAG-ASN : bond 0.00381 ( 14) link_NAG-ASN : angle 1.85349 ( 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 : 0.372 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: 0.1134 time to fit residues: 24.2675 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 : 0.390 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: H 31 ASN H 55 ASN H 155 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.208201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.167956 restraints weight = 13939.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.165683 restraints weight = 24518.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.167208 restraints weight = 21343.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.168358 restraints weight = 11983.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.169342 restraints weight = 9937.610| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10145 Z= 0.211 Angle : 0.758 9.622 13905 Z= 0.378 Chirality : 0.049 0.190 1634 Planarity : 0.005 0.063 1732 Dihedral : 11.655 67.949 1927 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.24 % Allowed : 8.67 % Favored : 90.09 % 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 aren not related in a simple way. whole: -1.18 (0.24), residues: 1241 helix: -1.46 (0.71), residues: 50 sheet: -0.03 (0.26), residues: 426 loop : -1.20 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 38 TYR 0.019 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 covalent geometry : bond 0.00505 (10096) covalent geometry : angle 0.74044 (13779) SS BOND : bond 0.00444 ( 21) SS BOND : angle 1.39115 ( 42) hydrogen bonds : bond 0.04583 ( 244) hydrogen bonds : angle 7.94816 ( 657) link_BETA1-4 : bond 0.00417 ( 14) link_BETA1-4 : angle 2.02180 ( 42) link_NAG-ASN : bond 0.00424 ( 14) link_NAG-ASN : angle 2.11870 ( 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 : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 431 ASP cc_start: 0.7973 (t0) cc_final: 0.7675 (t0) REVERT: E 579 LEU cc_start: 0.5848 (tp) cc_final: 0.5625 (tp) REVERT: A 309 TYR cc_start: 0.5398 (p90) cc_final: 0.4848 (p90) outliers start: 13 outliers final: 8 residues processed: 137 average time/residue: 0.1114 time to fit residues: 21.3891 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 : 0.387 ------------------------------------------------------------------------------- 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: 0.0270 chunk 46 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 0.0470 chunk 86 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 97 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 467 GLN ** 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 = 0.4499 r_free = 0.4499 target = 0.209560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.166319 restraints weight = 13856.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.167712 restraints weight = 21406.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.168967 restraints weight = 16548.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.169308 restraints weight = 10285.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.170508 restraints weight = 9019.760| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10145 Z= 0.118 Angle : 0.650 8.827 13905 Z= 0.319 Chirality : 0.046 0.181 1634 Planarity : 0.005 0.057 1732 Dihedral : 7.529 58.009 1927 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.33 % Allowed : 11.06 % Favored : 87.61 % 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 aren not related in a simple way. whole: -1.03 (0.24), residues: 1241 helix: -1.42 (0.73), residues: 50 sheet: 0.04 (0.26), residues: 424 loop : -1.08 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 94 TYR 0.016 0.001 TYR C 194 PHE 0.012 0.001 PHE B 139 TRP 0.024 0.001 TRP E 646 HIS 0.004 0.001 HIS H 200 Details of bonding type rmsd covalent geometry : bond 0.00271 (10096) covalent geometry : angle 0.63272 (13779) SS BOND : bond 0.00267 ( 21) SS BOND : angle 0.95211 ( 42) hydrogen bonds : bond 0.03578 ( 244) hydrogen bonds : angle 6.97525 ( 657) link_BETA1-4 : bond 0.00442 ( 14) link_BETA1-4 : angle 1.98859 ( 42) link_NAG-ASN : bond 0.00370 ( 14) link_NAG-ASN : angle 1.87690 ( 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 150 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7904 (pp30) cc_final: 0.7336 (pp30) REVERT: E 579 LEU cc_start: 0.5876 (tp) cc_final: 0.5625 (tp) REVERT: E 610 ASP cc_start: 0.7907 (t0) cc_final: 0.7462 (t70) REVERT: H 91 TYR cc_start: 0.6870 (m-80) cc_final: 0.5457 (m-10) REVERT: L 139 PHE cc_start: 0.6478 (p90) cc_final: 0.6043 (p90) REVERT: B 185 TYR cc_start: 0.5622 (t80) cc_final: 0.5393 (t80) outliers start: 14 outliers final: 10 residues processed: 142 average time/residue: 0.1105 time to fit residues: 21.9015 Evaluate side-chains 133 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain A residue 246 LEU 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: 0.6980 chunk 51 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 467 GLN ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.205676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.161119 restraints weight = 13833.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.158574 restraints weight = 22852.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.160589 restraints weight = 19208.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.161308 restraints weight = 10919.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.163712 restraints weight = 8902.296| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10145 Z= 0.212 Angle : 0.723 10.225 13905 Z= 0.360 Chirality : 0.047 0.208 1634 Planarity : 0.005 0.055 1732 Dihedral : 6.150 52.927 1927 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.48 % Allowed : 13.25 % Favored : 84.27 % 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 aren not related in a simple way. whole: -1.34 (0.23), residues: 1241 helix: -1.73 (0.66), residues: 50 sheet: -0.16 (0.25), residues: 440 loop : -1.31 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 630 TYR 0.022 0.002 TYR B 91 PHE 0.021 0.002 PHE E 509 TRP 0.019 0.002 TRP C 47 HIS 0.004 0.001 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00511 (10096) covalent geometry : angle 0.70687 (13779) SS BOND : bond 0.00455 ( 21) SS BOND : angle 1.24168 ( 42) hydrogen bonds : bond 0.03534 ( 244) hydrogen bonds : angle 6.76719 ( 657) link_BETA1-4 : bond 0.00413 ( 14) link_BETA1-4 : angle 1.84977 ( 42) link_NAG-ASN : bond 0.00448 ( 14) link_NAG-ASN : angle 2.02546 ( 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 155 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7957 (pp30) cc_final: 0.7394 (pp30) REVERT: E 610 ASP cc_start: 0.8067 (t0) cc_final: 0.7563 (t70) REVERT: E 644 CYS cc_start: 0.6971 (t) cc_final: 0.6542 (t) REVERT: E 656 ASP cc_start: 0.7912 (t0) cc_final: 0.7513 (t0) REVERT: A 219 MET cc_start: 0.6964 (tpp) cc_final: 0.6229 (ppp) outliers start: 26 outliers final: 20 residues processed: 148 average time/residue: 0.1001 time to fit residues: 21.1017 Evaluate side-chains 141 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 519 THR 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 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 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: 10.0000 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: 1.9990 chunk 8 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 107 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 638 HIS H 55 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.207474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.167094 restraints weight = 13966.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.170507 restraints weight = 25031.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.170487 restraints weight = 13162.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.170926 restraints weight = 9304.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.171542 restraints weight = 8165.292| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2428 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= 0.137 Angle : 0.645 9.613 13905 Z= 0.320 Chirality : 0.045 0.178 1634 Planarity : 0.005 0.060 1732 Dihedral : 5.625 55.831 1927 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.38 % Allowed : 14.78 % Favored : 82.84 % 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 aren not related in a simple way. whole: -1.25 (0.23), residues: 1241 helix: -1.49 (0.70), residues: 50 sheet: -0.11 (0.25), residues: 425 loop : -1.24 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 521 TYR 0.012 0.001 TYR B 185 PHE 0.016 0.002 PHE L 139 TRP 0.041 0.002 TRP E 646 HIS 0.003 0.001 HIS E 589 Details of bonding type rmsd covalent geometry : bond 0.00327 (10096) covalent geometry : angle 0.63144 (13779) SS BOND : bond 0.00298 ( 21) SS BOND : angle 1.05784 ( 42) hydrogen bonds : bond 0.03156 ( 244) hydrogen bonds : angle 6.48743 ( 657) link_BETA1-4 : bond 0.00428 ( 14) link_BETA1-4 : angle 1.56378 ( 42) link_NAG-ASN : bond 0.00350 ( 14) link_NAG-ASN : angle 1.83513 ( 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 : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7917 (pp30) cc_final: 0.7360 (pp30) REVERT: E 610 ASP cc_start: 0.7985 (t0) cc_final: 0.7560 (t70) REVERT: E 644 CYS cc_start: 0.6715 (t) cc_final: 0.6287 (t) REVERT: E 656 ASP cc_start: 0.7731 (t0) cc_final: 0.7436 (t0) REVERT: A 219 MET cc_start: 0.6920 (tpp) cc_final: 0.6406 (ppp) REVERT: B 4 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7825 (mm) outliers start: 25 outliers final: 18 residues processed: 148 average time/residue: 0.0933 time to fit residues: 20.1773 Evaluate side-chains 147 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 55 ASN 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 0.0770 chunk 103 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 101 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 63 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN ** 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 = 0.4484 r_free = 0.4484 target = 0.209281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.167813 restraints weight = 13914.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.171243 restraints weight = 23772.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.171473 restraints weight = 14059.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.172320 restraints weight = 9286.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.173070 restraints weight = 8094.764| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2571 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= 0.121 Angle : 0.625 9.054 13905 Z= 0.311 Chirality : 0.044 0.182 1634 Planarity : 0.005 0.057 1732 Dihedral : 5.376 59.869 1927 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.29 % Allowed : 15.92 % Favored : 81.79 % 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 aren not related in a simple way. whole: -1.16 (0.23), residues: 1241 helix: -1.33 (0.72), residues: 50 sheet: -0.05 (0.25), residues: 426 loop : -1.17 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 630 TYR 0.012 0.001 TYR B 191 PHE 0.030 0.002 PHE L 139 TRP 0.052 0.002 TRP E 646 HIS 0.002 0.001 HIS E 589 Details of bonding type rmsd covalent geometry : bond 0.00288 (10096) covalent geometry : angle 0.61356 (13779) SS BOND : bond 0.00315 ( 21) SS BOND : angle 0.91208 ( 42) hydrogen bonds : bond 0.02876 ( 244) hydrogen bonds : angle 6.23938 ( 657) link_BETA1-4 : bond 0.00428 ( 14) link_BETA1-4 : angle 1.45545 ( 42) link_NAG-ASN : bond 0.00342 ( 14) link_NAG-ASN : angle 1.71845 ( 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 159 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7882 (pp30) cc_final: 0.7317 (pp30) REVERT: E 579 LEU cc_start: 0.5889 (tp) cc_final: 0.5676 (tp) REVERT: E 644 CYS cc_start: 0.6680 (t) cc_final: 0.6296 (t) REVERT: L 38 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 219 MET cc_start: 0.6992 (tpp) cc_final: 0.6434 (ppp) REVERT: B 96 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8032 (pt) REVERT: B 139 PHE cc_start: 0.5924 (p90) cc_final: 0.5701 (p90) REVERT: C 66 GLN cc_start: 0.6852 (tm-30) cc_final: 0.6498 (tm-30) outliers start: 24 outliers final: 18 residues processed: 153 average time/residue: 0.0947 time to fit residues: 21.1476 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 : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 607 CYS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 169 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 101 optimal weight: 0.4980 chunk 80 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 106 optimal weight: 0.0270 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 23 optimal weight: 0.0170 chunk 79 optimal weight: 2.9990 overall best weight: 0.8678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.208809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.164760 restraints weight = 13789.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.166907 restraints weight = 22024.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.167892 restraints weight = 14870.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.167637 restraints weight = 10344.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.172141 restraints weight = 8307.675| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10145 Z= 0.145 Angle : 0.645 9.234 13905 Z= 0.321 Chirality : 0.045 0.176 1634 Planarity : 0.005 0.058 1732 Dihedral : 5.327 59.721 1927 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.96 % Allowed : 16.30 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.23), residues: 1241 helix: -1.21 (0.73), residues: 50 sheet: -0.16 (0.24), residues: 440 loop : -1.15 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 630 TYR 0.015 0.001 TYR B 191 PHE 0.019 0.002 PHE L 139 TRP 0.043 0.002 TRP E 646 HIS 0.003 0.001 HIS E 589 Details of bonding type rmsd covalent geometry : bond 0.00351 (10096) covalent geometry : angle 0.63415 (13779) SS BOND : bond 0.00344 ( 21) SS BOND : angle 0.99559 ( 42) hydrogen bonds : bond 0.02878 ( 244) hydrogen bonds : angle 6.10272 ( 657) link_BETA1-4 : bond 0.00431 ( 14) link_BETA1-4 : angle 1.43059 ( 42) link_NAG-ASN : bond 0.00360 ( 14) link_NAG-ASN : angle 1.68040 ( 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 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7905 (pp30) cc_final: 0.7328 (pp30) REVERT: E 563 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8144 (m) REVERT: E 579 LEU cc_start: 0.6115 (tp) cc_final: 0.5914 (tp) REVERT: E 610 ASP cc_start: 0.7832 (t70) cc_final: 0.7545 (t70) REVERT: E 644 CYS cc_start: 0.6688 (t) cc_final: 0.6286 (t) REVERT: L 82 ASP cc_start: 0.6358 (t0) cc_final: 0.5895 (t0) REVERT: A 219 MET cc_start: 0.7223 (tpp) cc_final: 0.6504 (ppp) REVERT: B 4 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7794 (mm) REVERT: B 96 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7992 (pt) REVERT: C 100 MET cc_start: 0.7847 (ttm) cc_final: 0.7500 (ttm) outliers start: 31 outliers final: 22 residues processed: 154 average time/residue: 0.0880 time to fit residues: 20.0766 Evaluate side-chains 152 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 52 SER Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain B residue 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 169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 123 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.205488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.159737 restraints weight = 13784.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155489 restraints weight = 21197.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.158313 restraints weight = 19366.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.158993 restraints weight = 10735.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.160755 restraints weight = 9216.310| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2939 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= 0.217 Angle : 0.718 9.986 13905 Z= 0.358 Chirality : 0.047 0.197 1634 Planarity : 0.005 0.056 1732 Dihedral : 5.695 51.682 1927 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.24 % Allowed : 16.59 % Favored : 80.17 % 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 aren not related in a simple way. whole: -1.37 (0.23), residues: 1241 helix: -1.24 (0.74), residues: 50 sheet: -0.32 (0.24), residues: 440 loop : -1.27 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 18 TYR 0.022 0.002 TYR B 91 PHE 0.023 0.002 PHE L 139 TRP 0.064 0.002 TRP E 646 HIS 0.005 0.001 HIS E 638 Details of bonding type rmsd covalent geometry : bond 0.00527 (10096) covalent geometry : angle 0.70622 (13779) SS BOND : bond 0.00425 ( 21) SS BOND : angle 1.21308 ( 42) hydrogen bonds : bond 0.03217 ( 244) hydrogen bonds : angle 6.17900 ( 657) link_BETA1-4 : bond 0.00409 ( 14) link_BETA1-4 : angle 1.51646 ( 42) link_NAG-ASN : bond 0.00436 ( 14) link_NAG-ASN : angle 1.85982 ( 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 163 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7915 (pp30) cc_final: 0.7345 (pp30) REVERT: E 610 ASP cc_start: 0.8021 (t70) cc_final: 0.7683 (t70) REVERT: E 644 CYS cc_start: 0.7024 (t) cc_final: 0.6643 (t) REVERT: E 656 ASP cc_start: 0.7848 (t0) cc_final: 0.7526 (t0) REVERT: L 47 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8370 (mt) REVERT: L 50 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7360 (mptt) REVERT: B 4 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7877 (mm) REVERT: B 96 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8064 (pt) REVERT: C 100 MET cc_start: 0.7913 (ttm) cc_final: 0.7594 (ttm) REVERT: C 204 ASN cc_start: 0.6626 (t0) cc_final: 0.6348 (t0) outliers start: 34 outliers final: 25 residues processed: 158 average time/residue: 0.0892 time to fit residues: 20.8319 Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 47 LEU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 THR 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 110 ILE Chi-restraints excluded: chain C residue 169 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** H 200 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 = 0.4428 r_free = 0.4428 target = 0.203948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157631 restraints weight = 13660.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.154451 restraints weight = 20131.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.156564 restraints weight = 18192.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.157445 restraints weight = 10124.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.162377 restraints weight = 8431.599| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10145 Z= 0.225 Angle : 0.738 14.049 13905 Z= 0.364 Chirality : 0.047 0.189 1634 Planarity : 0.005 0.058 1732 Dihedral : 5.850 45.537 1927 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % 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 : 0.09 % 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 aren not related in a simple way. whole: -1.49 (0.23), residues: 1241 helix: -1.77 (0.67), residues: 51 sheet: -0.39 (0.24), residues: 439 loop : -1.32 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 100G TYR 0.022 0.002 TYR B 91 PHE 0.027 0.002 PHE E 465 TRP 0.059 0.002 TRP E 646 HIS 0.005 0.001 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00545 (10096) covalent geometry : angle 0.72650 (13779) SS BOND : bond 0.00443 ( 21) SS BOND : angle 1.19878 ( 42) hydrogen bonds : bond 0.03245 ( 244) hydrogen bonds : angle 6.16806 ( 657) link_BETA1-4 : bond 0.00422 ( 14) link_BETA1-4 : angle 1.51355 ( 42) link_NAG-ASN : bond 0.00448 ( 14) link_NAG-ASN : angle 1.89138 ( 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 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7869 (pp30) cc_final: 0.7265 (pp30) REVERT: E 610 ASP cc_start: 0.8102 (t70) cc_final: 0.7747 (t70) REVERT: E 644 CYS cc_start: 0.7028 (t) cc_final: 0.6627 (t) REVERT: E 656 ASP cc_start: 0.7892 (t0) cc_final: 0.7630 (t0) REVERT: A 219 MET cc_start: 0.7097 (tpp) cc_final: 0.6610 (ppp) REVERT: B 4 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7919 (mm) REVERT: B 96 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8042 (pt) REVERT: C 100 MET cc_start: 0.7903 (ttm) cc_final: 0.7577 (ttm) outliers start: 31 outliers final: 27 residues processed: 154 average time/residue: 0.0927 time to fit residues: 21.0588 Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 677 CYS Chi-restraints excluded: chain E residue 699 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 106 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.206801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164260 restraints weight = 13649.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.167758 restraints weight = 22747.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.168002 restraints weight = 14190.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.167702 restraints weight = 10881.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.172869 restraints weight = 8509.411| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10145 Z= 0.141 Angle : 0.687 10.341 13905 Z= 0.339 Chirality : 0.046 0.243 1634 Planarity : 0.005 0.060 1732 Dihedral : 5.562 49.683 1927 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.76 % Allowed : 16.97 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.23), residues: 1241 helix: -1.54 (0.71), residues: 51 sheet: -0.30 (0.24), residues: 443 loop : -1.31 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 630 TYR 0.018 0.001 TYR E 527 PHE 0.017 0.002 PHE E 465 TRP 0.079 0.002 TRP E 646 HIS 0.003 0.001 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00344 (10096) covalent geometry : angle 0.67678 (13779) SS BOND : bond 0.00344 ( 21) SS BOND : angle 1.01307 ( 42) hydrogen bonds : bond 0.02819 ( 244) hydrogen bonds : angle 6.04763 ( 657) link_BETA1-4 : bond 0.00416 ( 14) link_BETA1-4 : angle 1.39730 ( 42) link_NAG-ASN : bond 0.00351 ( 14) link_NAG-ASN : angle 1.75201 ( 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 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 546 GLN cc_start: 0.7751 (pp30) cc_final: 0.7120 (pp30) REVERT: E 610 ASP cc_start: 0.7964 (t70) cc_final: 0.7658 (t70) REVERT: E 644 CYS cc_start: 0.6792 (t) cc_final: 0.6417 (t) REVERT: E 656 ASP cc_start: 0.7668 (t0) cc_final: 0.7394 (t0) REVERT: A 219 MET cc_start: 0.6886 (tpp) cc_final: 0.6483 (ppp) REVERT: B 4 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7854 (mm) REVERT: B 96 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8000 (pt) REVERT: C 100 MET cc_start: 0.7884 (ttm) cc_final: 0.7547 (ttm) outliers start: 29 outliers final: 23 residues processed: 154 average time/residue: 0.0977 time to fit residues: 21.4438 Evaluate side-chains 150 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 698 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 HIS H 55 ASN ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.206921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.163086 restraints weight = 13668.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.165622 restraints weight = 20832.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.166589 restraints weight = 13863.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.166470 restraints weight = 9481.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.168987 restraints weight = 8021.673| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10145 Z= 0.147 Angle : 0.682 10.681 13905 Z= 0.337 Chirality : 0.045 0.234 1634 Planarity : 0.005 0.059 1732 Dihedral : 5.493 52.667 1927 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % 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 aren not related in a simple way. whole: -1.34 (0.24), residues: 1241 helix: -1.22 (0.74), residues: 50 sheet: -0.26 (0.25), residues: 441 loop : -1.28 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 630 TYR 0.018 0.001 TYR E 527 PHE 0.017 0.002 PHE E 465 TRP 0.071 0.002 TRP E 646 HIS 0.003 0.001 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00360 (10096) covalent geometry : angle 0.67147 (13779) SS BOND : bond 0.00356 ( 21) SS BOND : angle 1.01327 ( 42) hydrogen bonds : bond 0.02802 ( 244) hydrogen bonds : angle 5.92630 ( 657) link_BETA1-4 : bond 0.00412 ( 14) link_BETA1-4 : angle 1.39294 ( 42) link_NAG-ASN : bond 0.00366 ( 14) link_NAG-ASN : angle 1.70171 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1740.52 seconds wall clock time: 31 minutes 3.58 seconds (1863.58 seconds total)