Starting phenix.real_space_refine on Fri Jul 3 20:45:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dfm_27408/07_2026/8dfm_27408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfm_27408/07_2026/8dfm_27408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dfm_27408/07_2026/8dfm_27408.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dfm_27408/07_2026/8dfm_27408.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dfm_27408/07_2026/8dfm_27408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfm_27408/07_2026/8dfm_27408.map" model { file = "/net/cci-nas-00/data/ceres_data/8dfm_27408/07_2026/8dfm_27408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfm_27408/07_2026/8dfm_27408.cif" } resolution = 3.45 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= -0.001 sd= 0.028 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: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 5385 2.51 5 N 1397 2.21 5 O 1578 1.98 5 H 7566 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15966 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 6105 Classifications: {'peptide': 441} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 421} Chain breaks: 3 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 5, 'ASP:plan': 9, 'GLU:plan': 23, 'GLN:plan1': 5, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 192 Chain: "B" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6095 Classifications: {'peptide': 446} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 342 Unresolved non-hydrogen angles: 415 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 13, 'ARG:plan': 5, 'GLU:plan': 21, 'GLN:plan1': 5, 'ASN:plan1': 6, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 208 Chain: "C" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1805 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1821 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 5, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.15, per 1000 atoms: 0.20 Number of scatterers: 15966 At special positions: 0 Unit cell: (74.03, 131.908, 187.094, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 O 1578 8.00 N 1397 7.00 C 5385 6.00 H 7566 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 186 " distance=2.04 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 428 " - pdb=" SG CYS A 491 " distance=2.04 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 186 " distance=2.04 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 491 " distance=2.05 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 89 " distance=2.01 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1001 " - " ASN A 283 " " NAG B1001 " - " ASN B 283 " " NAG E 1 " - " ASN A 300 " " NAG F 1 " - " ASN A 293 " " NAG G 1 " - " ASN B 293 " " NAG H 1 " - " ASN B 300 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 468.6 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 23 sheets defined 16.9% alpha, 44.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.088A pdb=" N GLY A 387 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.708A pdb=" N GLY B 387 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 12 Processing helix chain 'C' and resid 13 through 21 removed outlier: 4.454A pdb=" N LYS C 17 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 63 removed outlier: 4.581A pdb=" N TRP C 44 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 94 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'D' and resid 9 through 13 removed outlier: 3.667A pdb=" N VAL D 12 " --> pdb=" O THR D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 40 through 63 removed outlier: 4.064A pdb=" N TRP D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER D 46 " --> pdb=" O HIS D 42 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLU D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 94 Processing helix chain 'D' and resid 111 through 127 removed outlier: 3.819A pdb=" N LYS D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.652A pdb=" N SER A 38 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.661A pdb=" N LEU A 46 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG A 112 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 48 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 94 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 68 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR A 96 " --> pdb=" O TRP A 66 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP A 66 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR A 98 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 127 removed outlier: 7.027A pdb=" N LEU A 124 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ARG A 205 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLY A 126 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 189 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN A 145 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 127 removed outlier: 7.027A pdb=" N LEU A 124 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ARG A 205 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLY A 126 " --> pdb=" O ARG A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.627A pdb=" N LYS A 258 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 224 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 317 Processing sheet with id=AA9, first strand: chain 'A' and resid 322 through 326 removed outlier: 6.485A pdb=" N VAL A 323 " --> pdb=" O TYR A 408 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASN A 410 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 325 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LYS A 412 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 395 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 322 through 326 removed outlier: 6.485A pdb=" N VAL A 323 " --> pdb=" O TYR A 408 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASN A 410 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 325 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LYS A 412 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 433 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA A 431 " --> pdb=" O PRO A 413 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE A 415 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 429 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A 417 " --> pdb=" O GLN A 427 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN A 427 " --> pdb=" O THR A 417 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 437 through 443 removed outlier: 19.410A pdb=" N LYS A 499 " --> pdb=" O LYS B 499 " (cutoff:3.500A) removed outlier: 16.367A pdb=" N SER B 501 " --> pdb=" O LYS A 499 " (cutoff:3.500A) removed outlier: 11.672A pdb=" N SER A 501 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 10.595A pdb=" N TYR B 503 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR A 503 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ASN B 505 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASN A 505 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ALA B 507 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA A 507 " --> pdb=" O ALA B 507 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 487 " --> pdb=" O PHE B 506 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR B 488 " --> pdb=" O CYS B 443 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AB4, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.436A pdb=" N LEU B 46 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ARG B 112 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 48 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 94 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE B 68 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR B 96 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP B 66 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR B 98 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.600A pdb=" N GLY B 126 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 182 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP B 189 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASN B 145 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.600A pdb=" N GLY B 126 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 182 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 132 through 134 Processing sheet with id=AB8, first strand: chain 'B' and resid 213 through 216 Processing sheet with id=AB9, first strand: chain 'B' and resid 220 through 224 removed outlier: 7.628A pdb=" N TRP B 246 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR B 253 " --> pdb=" O TRP B 246 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 248 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 312 through 317 Processing sheet with id=AC2, first strand: chain 'B' and resid 322 through 326 removed outlier: 6.551A pdb=" N VAL B 323 " --> pdb=" O TYR B 408 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASN B 410 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 325 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 414 through 421 removed outlier: 6.547A pdb=" N VAL B 429 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR B 418 " --> pdb=" O GLN B 427 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLN B 427 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG B 420 " --> pdb=" O MET B 425 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET B 425 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS B 428 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AC5, first strand: chain 'D' and resid 28 through 31 397 hydrogen bonds defined for protein. 1005 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: 2.98 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 7562 1.03 - 1.23: 28 1.23 - 1.43: 3607 1.43 - 1.63: 4908 1.63 - 1.84: 52 Bond restraints: 16157 Sorted by residual: bond pdb=" C7 NAG F 2 " pdb=" N2 NAG F 2 " ideal model delta sigma weight residual 1.346 1.464 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C7 NAG B1001 " pdb=" N2 NAG B1001 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C7 NAG G 1 " pdb=" N2 NAG G 1 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C7 NAG G 2 " pdb=" N2 NAG G 2 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C7 NAG E 1 " pdb=" N2 NAG E 1 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.31e+01 ... (remaining 16152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 28454 2.76 - 5.52: 463 5.52 - 8.28: 29 8.28 - 11.04: 5 11.04 - 13.80: 1 Bond angle restraints: 28952 Sorted by residual: angle pdb=" N ASN A 293 " pdb=" CA ASN A 293 " pdb=" CB ASN A 293 " ideal model delta sigma weight residual 111.13 101.75 9.38 1.81e+00 3.05e-01 2.69e+01 angle pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " pdb=" C5 NAG F 1 " ideal model delta sigma weight residual 113.21 99.41 13.80 3.00e+00 1.11e-01 2.12e+01 angle pdb=" N GLY B 487 " pdb=" CA GLY B 487 " pdb=" C GLY B 487 " ideal model delta sigma weight residual 110.58 116.44 -5.86 1.35e+00 5.49e-01 1.89e+01 angle pdb=" C ASN B 486 " pdb=" N GLY B 487 " pdb=" CA GLY B 487 " ideal model delta sigma weight residual 121.28 111.65 9.63 2.26e+00 1.96e-01 1.82e+01 angle pdb=" CA CYS D 4 " pdb=" CB CYS D 4 " pdb=" SG CYS D 4 " ideal model delta sigma weight residual 114.40 104.92 9.48 2.30e+00 1.89e-01 1.70e+01 ... (remaining 28947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 6834 15.00 - 30.01: 643 30.01 - 45.01: 131 45.01 - 60.01: 144 60.01 - 75.02: 63 Dihedral angle restraints: 7815 sinusoidal: 3893 harmonic: 3922 Sorted by residual: dihedral pdb=" CA GLY B 487 " pdb=" C GLY B 487 " pdb=" N THR B 488 " pdb=" CA THR B 488 " ideal model delta harmonic sigma weight residual -180.00 -150.61 -29.39 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA PHE A 118 " pdb=" C PHE A 118 " pdb=" N LEU A 119 " pdb=" CA LEU A 119 " ideal model delta harmonic sigma weight residual 180.00 150.72 29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA LYS A 65 " pdb=" C LYS A 65 " pdb=" N TRP A 66 " pdb=" CA TRP A 66 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 7812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 1389 0.160 - 0.319: 33 0.319 - 0.479: 2 0.479 - 0.638: 0 0.638 - 0.798: 1 Chirality restraints: 1425 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 293 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" N2 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.86 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA ASN B 283 " pdb=" N ASN B 283 " pdb=" C ASN B 283 " pdb=" CB ASN B 283 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 1422 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 248 " 0.490 9.50e-02 1.11e+02 1.82e-01 1.74e+02 pdb=" NE ARG B 248 " 0.080 2.00e-02 2.50e+03 pdb=" CZ ARG B 248 " -0.072 2.00e-02 2.50e+03 pdb=" NH1 ARG B 248 " -0.128 2.00e-02 2.50e+03 pdb=" NH2 ARG B 248 " -0.098 2.00e-02 2.50e+03 pdb="HH11 ARG B 248 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG B 248 " 0.109 2.00e-02 2.50e+03 pdb="HH21 ARG B 248 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG B 248 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 224 " 0.395 9.50e-02 1.11e+02 1.54e-01 1.58e+02 pdb=" NE ARG A 224 " 0.084 2.00e-02 2.50e+03 pdb=" CZ ARG A 224 " -0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG A 224 " -0.119 2.00e-02 2.50e+03 pdb=" NH2 ARG A 224 " -0.096 2.00e-02 2.50e+03 pdb="HH11 ARG A 224 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 224 " 0.104 2.00e-02 2.50e+03 pdb="HH21 ARG A 224 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 224 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -0.337 9.50e-02 1.11e+02 1.35e-01 1.36e+02 pdb=" NE ARG A 248 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " 0.071 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " 0.132 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " 0.054 2.00e-02 2.50e+03 pdb="HH11 ARG A 248 " 0.010 2.00e-02 2.50e+03 pdb="HH12 ARG A 248 " -0.125 2.00e-02 2.50e+03 pdb="HH21 ARG A 248 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 248 " -0.050 2.00e-02 2.50e+03 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 488 2.17 - 2.78: 29593 2.78 - 3.38: 41265 3.38 - 3.99: 55264 3.99 - 4.60: 84877 Nonbonded interactions: 211487 Sorted by model distance: nonbonded pdb=" HG SER D 53 " pdb=" OD1 ASP D 84 " model vdw 1.561 2.450 nonbonded pdb=" HG SER C 53 " pdb=" OD1 ASP C 84 " model vdw 1.666 2.450 nonbonded pdb=" O VAL B 325 " pdb=" H ASN B 410 " model vdw 1.684 2.450 nonbonded pdb=" O PRO A 413 " pdb=" HG1 THR A 500 " model vdw 1.717 2.450 nonbonded pdb=" H ARG B 281 " pdb=" OD2 ASP B 284 " model vdw 1.719 2.450 ... (remaining 211482 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 'A' and (resid 36 through 44 or (resid 45 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 46 through 47 or (resid \ 48 through 49 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 50 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 61 through 63 or (resid 6 \ 4 through 65 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 66 through 78 or (resid 79 through 81 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 82 through 100 \ or (resid 101 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 102 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 128 through 184 or (re \ sid 185 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 186 through 217 or (resid 2 \ 18 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 219 through 227 or (resid 228 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 229 through 265 or (resid 266 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 267 through 326 or (resid 327 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 328 through 350 or (resid 351 through 3 \ 54 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 355 or (resid 356 through 358 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 359 or (resid 360 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 361 thro \ ugh 369 or (resid 370 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 371 through 375 or (resid 376 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 377 through 39 \ 7 or (resid 398 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 399 through 416 or (resid 417 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 418 through 471 or ( \ resid 472 through 473 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 474 through 478 or (resid 479 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 480 through 48 \ 1 or resid 486 through 491 or (resid 492 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 493 through 509 or resid 1001)) selection = (chain 'B' and (resid 36 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 56 through 73 \ or (resid 74 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 75 through 83 or (resid 84 through 86 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 87 through 148 \ or (resid 149 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 150 through 188 or (resid 189 through 191 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 192 throu \ gh 226 or (resid 227 through 228 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 229 through 252 or (resid 253 through 25 \ 4 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 255 through 317 or (resid 318 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 319 through 328 or (resid 329 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 330 through 335 or (resid 336 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 337 through 353 or (resid 354 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 355 \ through 420 or (resid 425 through 427 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 428 through 438 or (resid 439 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 440 through 441 or (resid 442 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 443 or resid 471 through 477 or (resid 4 \ 78 through 479 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 480 through 489 or (resid 490 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 491 through 1001)) } ncs_group { reference = (chain 'C' and (resid 3 through 57 or (resid 58 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 59 through 90 or (resid 9 \ 1 through 93 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 94 through 130)) selection = (chain 'D' and (resid 3 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 7 through 23 or (resid 24 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 25 through 37 or (resid 38 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 39 through 53 or (resid 54 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 55 thr \ ough 94 or resid 104 through 130)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.060 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: 0.120 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.380 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.008 0.118 8613 Z= 0.420 Angle : 1.165 14.834 11811 Z= 0.651 Chirality : 0.068 0.798 1425 Planarity : 0.012 0.152 1482 Dihedral : 12.276 75.019 2807 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.23), residues: 1104 helix: -0.98 (0.34), residues: 125 sheet: 0.90 (0.21), residues: 486 loop : -1.24 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.007 ARG B 135 TYR 0.060 0.009 TYR A 259 PHE 0.040 0.005 PHE B 506 TRP 0.037 0.008 TRP B 66 HIS 0.015 0.004 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00804 / 0.42 ( 8591) covalent geometry : angle 1.14185 / 0.65 (11757) SS BOND : bond 0.00961 / 0.64 ( 12) SS BOND : angle 1.33738 / 0.83 ( 24) hydrogen bonds : bond 0.16541 / 11.17 ( 390) hydrogen bonds : angle 7.89400 / 5.62 ( 1005) link_BETA1-4 : bond 0.00246 / 0.17 ( 4) link_BETA1-4 : angle 2.37678 / 1.54 ( 12) link_NAG-ASN : bond 0.00659 / 0.41 ( 6) link_NAG-ASN : angle 5.73745 / 3.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue THR 74 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue THR 417 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8299 (tt0) REVERT: C 88 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8667 (tm-30) REVERT: D 77 ASP cc_start: 0.8834 (t0) cc_final: 0.8626 (t0) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1728 time to fit residues: 13.1618 Evaluate side-chains 36 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 272 GLN B 272 GLN C 51 GLN D 21 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.050740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.043024 restraints weight = 137902.611| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.88 r_work: 0.3013 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8613 Z= 0.201 Angle : 0.693 9.266 11811 Z= 0.370 Chirality : 0.048 0.241 1425 Planarity : 0.004 0.040 1482 Dihedral : 6.916 30.463 1193 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.36 % Allowed : 4.96 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.24), residues: 1104 helix: 0.77 (0.42), residues: 136 sheet: 1.22 (0.23), residues: 471 loop : -0.58 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 205 TYR 0.016 0.002 TYR C 32 PHE 0.018 0.002 PHE C 116 TRP 0.017 0.002 TRP A 66 HIS 0.007 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 ( 8591) covalent geometry : angle 0.67011 / 0.37 (11757) SS BOND : bond 0.00482 / 0.32 ( 12) SS BOND : angle 0.90394 / 0.53 ( 24) hydrogen bonds : bond 0.04946 / 3.37 ( 390) hydrogen bonds : angle 6.23829 / 4.44 ( 1005) link_BETA1-4 : bond 0.00501 / 0.31 ( 4) link_BETA1-4 : angle 2.26825 / 1.60 ( 12) link_NAG-ASN : bond 0.00290 / 0.15 ( 6) link_NAG-ASN : angle 4.11204 / 2.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue THR 74 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue THR 417 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8427 (pt0) REVERT: C 88 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8784 (tm-30) REVERT: D 77 ASP cc_start: 0.8939 (t0) cc_final: 0.8499 (t0) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.1207 time to fit residues: 7.9902 Evaluate side-chains 36 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 68 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.050805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.043314 restraints weight = 141107.908| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.82 r_work: 0.3001 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8613 Z= 0.155 Angle : 0.580 8.506 11811 Z= 0.309 Chirality : 0.045 0.239 1425 Planarity : 0.003 0.030 1482 Dihedral : 5.848 26.950 1193 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.36 % Allowed : 6.05 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1104 helix: 1.66 (0.44), residues: 130 sheet: 1.06 (0.23), residues: 486 loop : -0.25 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.016 0.001 TYR A 350 PHE 0.015 0.001 PHE C 116 TRP 0.016 0.001 TRP A 66 HIS 0.002 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 8591) covalent geometry : angle 0.56447 / 0.31 (11757) SS BOND : bond 0.00315 / 0.21 ( 12) SS BOND : angle 0.52101 / 0.30 ( 24) hydrogen bonds : bond 0.04153 / 2.84 ( 390) hydrogen bonds : angle 5.58298 / 3.96 ( 1005) link_BETA1-4 : bond 0.00262 / 0.16 ( 4) link_BETA1-4 : angle 1.36520 / 0.88 ( 12) link_NAG-ASN : bond 0.00109 / 0.07 ( 6) link_NAG-ASN : angle 3.36250 / 2.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue THR 74 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue THR 417 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8528 (pt0) REVERT: C 88 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8748 (tm-30) REVERT: D 77 ASP cc_start: 0.8924 (t0) cc_final: 0.8481 (t0) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.1297 time to fit residues: 8.0358 Evaluate side-chains 34 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain C residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 0.0770 chunk 76 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.050102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.042439 restraints weight = 139755.051| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.85 r_work: 0.2992 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8613 Z= 0.177 Angle : 0.560 8.363 11811 Z= 0.297 Chirality : 0.044 0.194 1425 Planarity : 0.004 0.041 1482 Dihedral : 5.507 25.657 1193 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.60 % Allowed : 6.05 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.25), residues: 1104 helix: 1.72 (0.44), residues: 130 sheet: 0.94 (0.23), residues: 489 loop : -0.07 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.009 0.001 TYR A 350 PHE 0.013 0.001 PHE C 116 TRP 0.011 0.001 TRP A 66 HIS 0.002 0.001 HIS A 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 ( 8591) covalent geometry : angle 0.54432 / 0.29 (11757) SS BOND : bond 0.00331 / 0.22 ( 12) SS BOND : angle 0.51622 / 0.30 ( 24) hydrogen bonds : bond 0.03707 / 2.56 ( 390) hydrogen bonds : angle 5.37401 / 3.81 ( 1005) link_BETA1-4 : bond 0.00269 / 0.15 ( 4) link_BETA1-4 : angle 1.41265 / 0.92 ( 12) link_NAG-ASN : bond 0.00122 / 0.07 ( 6) link_NAG-ASN : angle 3.26238 / 2.25 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue THR 74 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue THR 417 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 36 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8446 (mt-10) REVERT: C 88 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8619 (tm-30) REVERT: D 77 ASP cc_start: 0.8935 (t0) cc_final: 0.8501 (t0) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.1063 time to fit residues: 6.7007 Evaluate side-chains 35 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 89 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.049858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.042278 restraints weight = 141954.460| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.85 r_work: 0.2985 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8613 Z= 0.164 Angle : 0.523 8.232 11811 Z= 0.276 Chirality : 0.044 0.213 1425 Planarity : 0.003 0.031 1482 Dihedral : 5.000 22.898 1193 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.36 % Allowed : 6.53 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.25), residues: 1104 helix: 1.82 (0.45), residues: 131 sheet: 0.87 (0.23), residues: 485 loop : 0.05 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 181 TYR 0.007 0.001 TYR A 350 PHE 0.012 0.001 PHE C 116 TRP 0.010 0.001 TRP A 66 HIS 0.002 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 8591) covalent geometry : angle 0.50932 / 0.27 (11757) SS BOND : bond 0.00306 / 0.20 ( 12) SS BOND : angle 0.42909 / 0.25 ( 24) hydrogen bonds : bond 0.03372 / 2.33 ( 390) hydrogen bonds : angle 5.03350 / 3.56 ( 1005) link_BETA1-4 : bond 0.00159 / 0.11 ( 4) link_BETA1-4 : angle 1.30663 / 0.82 ( 12) link_NAG-ASN : bond 0.00154 / 0.08 ( 6) link_NAG-ASN : angle 2.97582 / 2.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue THR 74 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue THR 417 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 36 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8637 (tm-30) REVERT: D 77 ASP cc_start: 0.8904 (t0) cc_final: 0.8477 (t0) outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.1229 time to fit residues: 7.6705 Evaluate side-chains 35 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 89 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 0.0980 chunk 110 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 38 optimal weight: 0.0050 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 89 optimal weight: 0.6980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.050194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.042419 restraints weight = 139865.113| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.91 r_work: 0.3002 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8613 Z= 0.097 Angle : 0.496 8.253 11811 Z= 0.258 Chirality : 0.045 0.192 1425 Planarity : 0.003 0.030 1482 Dihedral : 4.740 21.122 1193 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.60 % Allowed : 6.65 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.26), residues: 1104 helix: 2.13 (0.46), residues: 131 sheet: 0.84 (0.23), residues: 481 loop : 0.16 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.007 0.001 TYR B 291 PHE 0.010 0.001 PHE C 119 TRP 0.010 0.001 TRP A 66 HIS 0.002 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 8591) covalent geometry : angle 0.48145 / 0.26 (11757) SS BOND : bond 0.00249 / 0.17 ( 12) SS BOND : angle 0.52322 / 0.31 ( 24) hydrogen bonds : bond 0.03109 / 2.15 ( 390) hydrogen bonds : angle 4.77782 / 3.39 ( 1005) link_BETA1-4 : bond 0.00280 / 0.19 ( 4) link_BETA1-4 : angle 1.26012 / 0.80 ( 12) link_NAG-ASN : bond 0.00251 / 0.16 ( 6) link_NAG-ASN : angle 2.95874 / 2.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue THR 74 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue THR 417 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 289 MET cc_start: 0.8842 (ttm) cc_final: 0.8640 (ttt) REVERT: C 88 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8557 (tm-30) REVERT: D 77 ASP cc_start: 0.8837 (t0) cc_final: 0.8398 (t0) outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.1349 time to fit residues: 7.6713 Evaluate side-chains 35 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 89 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.049085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.041319 restraints weight = 141007.305| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.87 r_work: 0.2949 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8613 Z= 0.218 Angle : 0.540 10.675 11811 Z= 0.280 Chirality : 0.043 0.209 1425 Planarity : 0.003 0.031 1482 Dihedral : 4.771 20.830 1193 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.73 % Allowed : 7.01 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.26), residues: 1104 helix: 1.95 (0.46), residues: 131 sheet: 0.72 (0.23), residues: 481 loop : 0.12 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 117 TYR 0.007 0.001 TYR A 146 PHE 0.013 0.001 PHE C 116 TRP 0.006 0.001 TRP B 246 HIS 0.002 0.001 HIS A 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 ( 8591) covalent geometry : angle 0.52547 / 0.28 (11757) SS BOND : bond 0.00262 / 0.16 ( 12) SS BOND : angle 0.47013 / 0.28 ( 24) hydrogen bonds : bond 0.03329 / 2.31 ( 390) hydrogen bonds : angle 4.92757 / 3.47 ( 1005) link_BETA1-4 : bond 0.00109 / 0.07 ( 4) link_BETA1-4 : angle 1.36530 / 0.85 ( 12) link_NAG-ASN : bond 0.00316 / 0.15 ( 6) link_NAG-ASN : angle 3.02118 / 2.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue THR 74 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue THR 417 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8623 (tm-30) REVERT: D 77 ASP cc_start: 0.8915 (t0) cc_final: 0.8496 (t0) outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 0.1131 time to fit residues: 7.1736 Evaluate side-chains 35 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 89 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 90 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.049389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.041640 restraints weight = 141566.502| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.89 r_work: 0.2962 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8613 Z= 0.129 Angle : 0.505 9.676 11811 Z= 0.261 Chirality : 0.044 0.199 1425 Planarity : 0.003 0.030 1482 Dihedral : 4.635 19.787 1193 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.73 % Allowed : 7.26 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1104 helix: 2.05 (0.47), residues: 131 sheet: 0.71 (0.23), residues: 479 loop : 0.13 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 117 TYR 0.006 0.001 TYR A 350 PHE 0.011 0.001 PHE C 119 TRP 0.008 0.001 TRP A 66 HIS 0.003 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8591) covalent geometry : angle 0.49070 / 0.26 (11757) SS BOND : bond 0.00232 / 0.14 ( 12) SS BOND : angle 0.45555 / 0.27 ( 24) hydrogen bonds : bond 0.03184 / 2.21 ( 390) hydrogen bonds : angle 4.72360 / 3.34 ( 1005) link_BETA1-4 : bond 0.00224 / 0.14 ( 4) link_BETA1-4 : angle 1.21445 / 0.74 ( 12) link_NAG-ASN : bond 0.00162 / 0.11 ( 6) link_NAG-ASN : angle 2.93198 / 2.08 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue THR 74 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue THR 417 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8577 (tm-30) REVERT: D 77 ASP cc_start: 0.8893 (t0) cc_final: 0.8450 (t0) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.1166 time to fit residues: 7.1898 Evaluate side-chains 36 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 89 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 57 optimal weight: 0.0870 chunk 108 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 55 optimal weight: 0.7980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.049568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.041806 restraints weight = 139967.633| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.87 r_work: 0.2970 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8613 Z= 0.108 Angle : 0.498 9.902 11811 Z= 0.256 Chirality : 0.044 0.197 1425 Planarity : 0.003 0.030 1482 Dihedral : 4.545 19.243 1193 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.60 % Allowed : 7.38 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.26), residues: 1104 helix: 2.13 (0.47), residues: 131 sheet: 0.73 (0.23), residues: 479 loop : 0.21 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 117 TYR 0.007 0.001 TYR A 350 PHE 0.011 0.001 PHE C 119 TRP 0.009 0.001 TRP A 66 HIS 0.002 0.000 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8591) covalent geometry : angle 0.48467 / 0.25 (11757) SS BOND : bond 0.00230 / 0.14 ( 12) SS BOND : angle 0.44572 / 0.26 ( 24) hydrogen bonds : bond 0.03081 / 2.13 ( 390) hydrogen bonds : angle 4.65428 / 3.29 ( 1005) link_BETA1-4 : bond 0.00229 / 0.15 ( 4) link_BETA1-4 : angle 1.18668 / 0.72 ( 12) link_NAG-ASN : bond 0.00173 / 0.12 ( 6) link_NAG-ASN : angle 2.88703 / 2.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue THR 74 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue THR 417 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 35 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8555 (tm-30) REVERT: D 77 ASP cc_start: 0.8870 (t0) cc_final: 0.8432 (t0) outliers start: 5 outliers final: 5 residues processed: 35 average time/residue: 0.1274 time to fit residues: 7.7791 Evaluate side-chains 35 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.049437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.041655 restraints weight = 140224.756| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.89 r_work: 0.2963 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8613 Z= 0.142 Angle : 0.514 10.488 11811 Z= 0.262 Chirality : 0.043 0.198 1425 Planarity : 0.003 0.030 1482 Dihedral : 4.530 18.904 1193 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.60 % Allowed : 7.50 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.26), residues: 1104 helix: 2.09 (0.46), residues: 131 sheet: 0.74 (0.24), residues: 473 loop : 0.17 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 117 TYR 0.008 0.001 TYR A 350 PHE 0.011 0.001 PHE C 119 TRP 0.006 0.001 TRP B 246 HIS 0.002 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 8591) covalent geometry : angle 0.50063 / 0.26 (11757) SS BOND : bond 0.00233 / 0.14 ( 12) SS BOND : angle 0.44195 / 0.26 ( 24) hydrogen bonds : bond 0.03102 / 2.16 ( 390) hydrogen bonds : angle 4.64834 / 3.28 ( 1005) link_BETA1-4 : bond 0.00193 / 0.13 ( 4) link_BETA1-4 : angle 1.18644 / 0.71 ( 12) link_NAG-ASN : bond 0.00174 / 0.10 ( 6) link_NAG-ASN : angle 2.89369 / 2.05 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue THR 74 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue THR 417 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue VAL 473 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 35 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 MET cc_start: 0.8549 (tpt) cc_final: 0.8272 (tpp) REVERT: C 88 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8569 (tm-30) REVERT: D 77 ASP cc_start: 0.8886 (t0) cc_final: 0.8457 (t0) outliers start: 5 outliers final: 5 residues processed: 35 average time/residue: 0.1084 time to fit residues: 6.6077 Evaluate side-chains 35 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 102 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 47 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 0.2678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.049773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.042030 restraints weight = 139185.434| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.88 r_work: 0.2979 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8613 Z= 0.089 Angle : 0.498 10.742 11811 Z= 0.252 Chirality : 0.044 0.198 1425 Planarity : 0.003 0.031 1482 Dihedral : 4.386 17.991 1193 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.36 % Allowed : 7.74 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.26), residues: 1104 helix: 2.21 (0.47), residues: 131 sheet: 0.73 (0.24), residues: 481 loop : 0.32 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 117 TYR 0.008 0.001 TYR A 350 PHE 0.011 0.001 PHE C 119 TRP 0.010 0.001 TRP A 66 HIS 0.002 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 ( 8591) covalent geometry : angle 0.48519 / 0.25 (11757) SS BOND : bond 0.00210 / 0.14 ( 12) SS BOND : angle 0.43493 / 0.25 ( 24) hydrogen bonds : bond 0.02927 / 2.04 ( 390) hydrogen bonds : angle 4.44920 / 3.15 ( 1005) link_BETA1-4 : bond 0.00278 / 0.18 ( 4) link_BETA1-4 : angle 1.09029 / 0.64 ( 12) link_NAG-ASN : bond 0.00223 / 0.16 ( 6) link_NAG-ASN : angle 2.78129 / 2.00 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3131.02 seconds wall clock time: 53 minutes 52.87 seconds (3232.87 seconds total)