Starting phenix.real_space_refine on Fri Feb 16 17:07:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfm_27408/02_2024/8dfm_27408.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfm_27408/02_2024/8dfm_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfm_27408/02_2024/8dfm_27408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfm_27408/02_2024/8dfm_27408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfm_27408/02_2024/8dfm_27408.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfm_27408/02_2024/8dfm_27408.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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 Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'GLN:plan1': 5, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 23, 'ARG:plan': 5} 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: {'GLN:plan1': 5, 'HIS:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 5} 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: {'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP: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: {'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.11, per 1000 atoms: 0.45 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 12.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.52 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: 6.09 Time building geometry restraints manager: 12.72 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: 99.41 - 106.37: 385 106.37 - 113.32: 18232 113.32 - 120.28: 5201 120.28 - 127.24: 5024 127.24 - 134.20: 110 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: 6998 15.00 - 30.01: 679 30.01 - 45.01: 140 45.01 - 60.01: 145 60.01 - 75.02: 63 Dihedral angle restraints: 8025 sinusoidal: 4103 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 8022 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 1.850 nonbonded pdb=" HG SER C 53 " pdb=" OD1 ASP C 84 " model vdw 1.666 1.850 nonbonded pdb=" O VAL B 325 " pdb=" H ASN B 410 " model vdw 1.684 1.850 nonbonded pdb=" O PRO A 413 " pdb=" HG1 THR A 500 " model vdw 1.717 1.850 nonbonded pdb=" H ARG B 281 " pdb=" OD2 ASP B 284 " model vdw 1.719 1.850 ... (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 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 509 or re \ sid 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: 4.370 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: 0.270 Extract box with map and model: 19.990 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 52.080 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 8591 Z= 0.527 Angle : 1.142 13.803 11757 Z= 0.647 Chirality : 0.068 0.798 1425 Planarity : 0.012 0.152 1482 Dihedral : 12.317 75.019 3017 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (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 TRP 0.037 0.008 TRP B 66 HIS 0.015 0.004 HIS B 378 PHE 0.040 0.005 PHE B 506 TYR 0.060 0.009 TYR A 259 ARG 0.037 0.007 ARG B 135 *********************** 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 fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.525 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: 0.8320 (pt0) REVERT: C 88 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8667 (tm-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.4717 time to fit residues: 34.4948 Evaluate side-chains 35 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.0270 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 272 GLN B 272 GLN C 51 GLN D 21 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8591 Z= 0.249 Angle : 0.653 6.368 11757 Z= 0.357 Chirality : 0.048 0.199 1425 Planarity : 0.004 0.038 1482 Dihedral : 7.374 59.992 1403 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.36 % Allowed : 4.84 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1104 helix: 0.78 (0.42), residues: 136 sheet: 1.20 (0.23), residues: 475 loop : -0.51 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 66 HIS 0.005 0.001 HIS A 345 PHE 0.019 0.002 PHE C 116 TYR 0.014 0.002 TYR C 32 ARG 0.005 0.001 ARG C 117 *********************** 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 40 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 1.411 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: symmetry clash REVERT: C 88 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8673 (tm-30) outliers start: 3 outliers final: 1 residues processed: 39 average time/residue: 0.2951 time to fit residues: 19.1029 Evaluate side-chains 34 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8591 Z= 0.249 Angle : 0.556 5.255 11757 Z= 0.302 Chirality : 0.045 0.218 1425 Planarity : 0.003 0.028 1482 Dihedral : 6.531 57.869 1403 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.24 % Allowed : 6.05 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1104 helix: 1.61 (0.45), residues: 130 sheet: 1.12 (0.23), residues: 482 loop : -0.14 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 66 HIS 0.003 0.001 HIS A 378 PHE 0.016 0.001 PHE C 116 TYR 0.015 0.001 TYR A 350 ARG 0.003 0.000 ARG A 205 *********************** 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 35 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 1.359 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: 0.9096 (tm-30) cc_final: 0.8649 (tm-30) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.3005 time to fit residues: 17.9322 Evaluate side-chains 32 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 75 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8591 Z= 0.261 Angle : 0.538 10.734 11757 Z= 0.287 Chirality : 0.044 0.145 1425 Planarity : 0.003 0.029 1482 Dihedral : 5.929 43.898 1403 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.73 % Allowed : 6.29 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1104 helix: 1.80 (0.46), residues: 130 sheet: 1.06 (0.23), residues: 480 loop : -0.02 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 66 HIS 0.002 0.001 HIS A 263 PHE 0.014 0.001 PHE C 116 TYR 0.008 0.001 TYR A 373 ARG 0.003 0.000 ARG A 205 *********************** 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 35 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 1.293 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: C 88 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8517 (tm-30) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 0.2715 time to fit residues: 16.4510 Evaluate side-chains 33 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain B residue 130 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 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8591 Z= 0.250 Angle : 0.515 5.300 11757 Z= 0.278 Chirality : 0.043 0.177 1425 Planarity : 0.003 0.030 1482 Dihedral : 5.593 42.424 1403 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.48 % Allowed : 7.01 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1104 helix: 1.83 (0.46), residues: 131 sheet: 0.98 (0.23), residues: 479 loop : 0.05 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 66 HIS 0.002 0.001 HIS B 185 PHE 0.013 0.001 PHE C 116 TYR 0.007 0.001 TYR B 291 ARG 0.003 0.000 ARG B 181 *********************** 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 33 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 1.356 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: 0.9106 (tm-30) cc_final: 0.8506 (tm-30) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 0.2698 time to fit residues: 15.8254 Evaluate side-chains 32 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 107 optimal weight: 0.0970 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 56 optimal weight: 0.0070 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8591 Z= 0.132 Angle : 0.473 5.144 11757 Z= 0.252 Chirality : 0.044 0.160 1425 Planarity : 0.003 0.029 1482 Dihedral : 5.059 40.324 1403 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.36 % Allowed : 7.01 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1104 helix: 2.23 (0.47), residues: 131 sheet: 1.03 (0.23), residues: 477 loop : 0.31 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 66 HIS 0.002 0.000 HIS B 185 PHE 0.009 0.001 PHE C 119 TYR 0.008 0.001 TYR B 291 ARG 0.003 0.000 ARG A 205 *********************** 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 36 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 1.413 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: 0.9074 (tm-30) cc_final: 0.8455 (tm-30) outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.3739 time to fit residues: 20.5634 Evaluate side-chains 34 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 90 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8591 Z= 0.153 Angle : 0.481 8.853 11757 Z= 0.252 Chirality : 0.043 0.166 1425 Planarity : 0.003 0.029 1482 Dihedral : 4.930 41.142 1403 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.36 % Allowed : 7.13 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.26), residues: 1104 helix: 2.26 (0.47), residues: 131 sheet: 1.17 (0.23), residues: 466 loop : 0.28 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 66 HIS 0.002 0.000 HIS B 185 PHE 0.011 0.001 PHE C 119 TYR 0.007 0.001 TYR B 291 ARG 0.004 0.000 ARG C 117 *********************** 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 34 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 1.353 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 171 MET cc_start: 0.8462 (tpt) cc_final: 0.8203 (tpp) REVERT: C 88 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8447 (tm-30) outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.2750 time to fit residues: 16.2954 Evaluate side-chains 34 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 0.0270 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8591 Z= 0.209 Angle : 0.488 8.983 11757 Z= 0.256 Chirality : 0.043 0.169 1425 Planarity : 0.003 0.031 1482 Dihedral : 4.858 43.903 1403 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.60 % Allowed : 7.01 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1104 helix: 2.19 (0.47), residues: 131 sheet: 1.11 (0.23), residues: 467 loop : 0.27 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 66 HIS 0.002 0.001 HIS B 185 PHE 0.012 0.001 PHE C 116 TYR 0.005 0.001 TYR B 291 ARG 0.003 0.000 ARG C 117 *********************** 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 36 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 1.325 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: 0.8449 (tpt) cc_final: 0.8206 (tpp) REVERT: C 88 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8417 (tm-30) outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 0.2722 time to fit residues: 16.5050 Evaluate side-chains 33 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8591 Z= 0.296 Angle : 0.517 9.451 11757 Z= 0.272 Chirality : 0.043 0.174 1425 Planarity : 0.003 0.033 1482 Dihedral : 4.875 46.125 1403 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.36 % Allowed : 7.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1104 helix: 1.97 (0.47), residues: 131 sheet: 0.94 (0.23), residues: 467 loop : 0.22 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 66 HIS 0.003 0.001 HIS B 185 PHE 0.014 0.001 PHE C 116 TYR 0.008 0.001 TYR B 337 ARG 0.003 0.000 ARG C 117 *********************** 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 32 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 1.283 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: B 289 MET cc_start: 0.8847 (ttm) cc_final: 0.8642 (ttt) REVERT: C 88 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8426 (tm-30) REVERT: D 36 MET cc_start: 0.9013 (ppp) cc_final: 0.8592 (ppp) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.2766 time to fit residues: 15.7046 Evaluate side-chains 31 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 101 optimal weight: 0.2980 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8591 Z= 0.171 Angle : 0.498 9.975 11757 Z= 0.257 Chirality : 0.044 0.175 1425 Planarity : 0.003 0.034 1482 Dihedral : 4.756 44.535 1403 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1104 helix: 2.14 (0.48), residues: 131 sheet: 1.01 (0.24), residues: 466 loop : 0.28 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 66 HIS 0.002 0.000 HIS B 185 PHE 0.010 0.001 PHE C 119 TYR 0.008 0.001 TYR A 350 ARG 0.003 0.000 ARG C 117 ********************** 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 32 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 1.437 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: C 88 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8369 (tm-30) REVERT: D 36 MET cc_start: 0.8952 (ppp) cc_final: 0.8546 (ppp) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.2848 time to fit residues: 15.7169 Evaluate side-chains 32 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.0970 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.049310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.041578 restraints weight = 139731.631| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.86 r_work: 0.2959 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8591 Z= 0.229 Angle : 0.505 9.764 11757 Z= 0.262 Chirality : 0.043 0.175 1425 Planarity : 0.003 0.032 1482 Dihedral : 4.702 46.930 1403 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.36 % Allowed : 7.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1104 helix: 2.10 (0.47), residues: 131 sheet: 0.92 (0.24), residues: 465 loop : 0.25 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 246 HIS 0.002 0.001 HIS B 185 PHE 0.013 0.001 PHE C 116 TYR 0.010 0.001 TYR B 337 ARG 0.003 0.000 ARG C 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3678.86 seconds wall clock time: 66 minutes 9.02 seconds (3969.02 seconds total)