Starting phenix.real_space_refine on Wed Mar 4 18:20:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ki6_22885/03_2026/7ki6_22885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ki6_22885/03_2026/7ki6_22885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ki6_22885/03_2026/7ki6_22885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ki6_22885/03_2026/7ki6_22885.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ki6_22885/03_2026/7ki6_22885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ki6_22885/03_2026/7ki6_22885.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 9807 2.51 5 N 2478 2.21 5 O 3090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15453 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3324 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 927 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3324 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 927 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3324 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 927 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" 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: "J" 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: "K" 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: "M" 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: "N" 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: "O" 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: 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: "B" 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: "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 Time building chain proxies: 3.39, per 1000 atoms: 0.22 Number of scatterers: 15453 At special positions: 0 Unit cell: (128.1, 130.2, 105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3090 8.00 N 2478 7.00 C 9807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.01 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.09 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.01 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.09 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 87 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 192 " distance=2.04 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 355 " - pdb=" SG CYS E 363 " distance=2.01 Simple disulfide: pdb=" SG CYS E 387 " - pdb=" SG CYS E 392 " distance=2.09 Simple disulfide: pdb=" SG CYS E 394 " - pdb=" SG CYS E 417 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 87 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 99 " " NAG A 602 " - " ASN A 67 " " NAG B 601 " - " ASN B 99 " " NAG B 602 " - " ASN B 67 " " NAG E 601 " - " ASN E 99 " " NAG E 602 " - " ASN E 67 " " NAG I 1 " - " ASN A 414 " " NAG J 1 " - " ASN A 464 " " NAG K 1 " - " ASN B 414 " " NAG M 1 " - " ASN B 464 " " NAG N 1 " - " ASN E 414 " " NAG O 1 " - " ASN E 464 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 672.8 milliseconds 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3726 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 33 sheets defined 29.9% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 65 through 72 removed outlier: 6.151A pdb=" N LYS A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 Proline residue: A 89 - end of helix removed outlier: 3.785A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.885A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 191 through 215 removed outlier: 4.300A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.520A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 65 through 72 removed outlier: 6.151A pdb=" N LYS B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 Proline residue: B 89 - end of helix removed outlier: 3.785A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.885A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.301A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 452 through 471 removed outlier: 3.519A pdb=" N SER B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 29 through 35 Processing helix chain 'E' and resid 65 through 72 removed outlier: 6.151A pdb=" N LYS E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 Proline residue: E 89 - end of helix removed outlier: 3.786A pdb=" N TYR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.885A pdb=" N LYS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 153 Processing helix chain 'E' and resid 175 through 183 Processing helix chain 'E' and resid 184 through 187 Processing helix chain 'E' and resid 191 through 215 removed outlier: 4.300A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 233 through 236 Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 349 through 357 Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 437 through 441 Processing helix chain 'E' and resid 452 through 471 removed outlier: 3.519A pdb=" N SER E 457 " --> pdb=" O LYS E 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 164 removed outlier: 6.540A pdb=" N LYS A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 10.574A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 39 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU A 296 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY A 41 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN A 294 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR A 43 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR A 292 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N LYS A 45 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN A 290 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS A 47 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 288 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.119A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 277 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 288 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS A 47 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN A 290 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N LYS A 45 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR A 292 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR A 43 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN A 294 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY A 41 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU A 296 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 39 " --> pdb=" O LEU A 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.575A pdb=" N MET A 115 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 5 removed outlier: 5.484A pdb=" N THR L 68 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N SER L 27 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N SER L 66 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 11.339A pdb=" N VAL L 29 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 11.802A pdb=" N SER L 64 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.698A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.698A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.544A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY H 100 " --> pdb=" O MET H 106 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET H 106 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.544A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 158 through 164 removed outlier: 6.539A pdb=" N LYS B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 10.574A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 39 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU B 296 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY B 41 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 294 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR B 43 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR B 292 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N LYS B 45 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN B 290 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS B 47 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 288 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 275 through 298 current: chain 'B' and resid 332 through 333 Processing sheet with id=AB6, first strand: chain 'B' and resid 226 through 227 removed outlier: 4.119A pdb=" N MET B 226 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 277 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 288 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS B 47 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN B 290 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N LYS B 45 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR B 292 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR B 43 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 294 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY B 41 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU B 296 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 39 " --> pdb=" O LEU B 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 322 through 326 Processing sheet with id=AB7, first strand: chain 'B' and resid 101 through 102 removed outlier: 6.574A pdb=" N MET B 115 " --> pdb=" O SER E 428 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB9, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'C' and resid 4 through 5 removed outlier: 5.484A pdb=" N THR C 68 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N SER C 27 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N SER C 66 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N VAL C 29 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 11.802A pdb=" N SER C 64 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.698A pdb=" N MET C 11 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP C 34 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.698A pdb=" N MET C 11 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.544A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR D 108 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY D 100 " --> pdb=" O MET D 106 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N MET D 106 " --> pdb=" O GLY D 100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.544A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 158 through 164 removed outlier: 6.539A pdb=" N LYS E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 10.574A pdb=" N THR E 168 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP E 56 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR E 170 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL E 39 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU E 296 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY E 41 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN E 294 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR E 43 " --> pdb=" O TYR E 292 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR E 292 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N LYS E 45 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN E 290 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS E 47 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 288 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS E 49 " --> pdb=" O THR E 286 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR E 286 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN E 51 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 284 " --> pdb=" O ASN E 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 275 through 298 current: chain 'E' and resid 332 through 333 Processing sheet with id=AC8, first strand: chain 'E' and resid 226 through 227 removed outlier: 4.119A pdb=" N MET E 226 " --> pdb=" O GLY E 264 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 263 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE E 277 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL E 269 " --> pdb=" O TYR E 275 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR E 275 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 284 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN E 51 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR E 286 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS E 49 " --> pdb=" O THR E 286 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 288 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS E 47 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN E 290 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N LYS E 45 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR E 292 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR E 43 " --> pdb=" O TYR E 292 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN E 294 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY E 41 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU E 296 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL E 39 " --> pdb=" O LEU E 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 38 through 60 current: chain 'E' and resid 322 through 326 Processing sheet with id=AC9, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AD1, first strand: chain 'F' and resid 4 through 5 removed outlier: 5.485A pdb=" N THR F 68 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N SER F 27 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N SER F 66 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 11.339A pdb=" N VAL F 29 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 11.802A pdb=" N SER F 64 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.698A pdb=" N MET F 11 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP F 34 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.698A pdb=" N MET F 11 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.544A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR G 51 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP G 35 " --> pdb=" O TYR G 51 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR G 108 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY G 100 " --> pdb=" O MET G 106 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET G 106 " --> pdb=" O GLY G 100 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.544A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR G 51 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP G 35 " --> pdb=" O TYR G 51 " (cutoff:3.500A) 713 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3958 1.33 - 1.46: 4350 1.46 - 1.59: 7307 1.59 - 1.72: 9 1.72 - 1.85: 111 Bond restraints: 15735 Sorted by residual: bond pdb=" CG MET B 411 " pdb=" SD MET B 411 " ideal model delta sigma weight residual 1.803 1.717 0.086 2.50e-02 1.60e+03 1.19e+01 bond pdb=" CG MET A 411 " pdb=" SD MET A 411 " ideal model delta sigma weight residual 1.803 1.717 0.086 2.50e-02 1.60e+03 1.18e+01 bond pdb=" NE ARG E 365 " pdb=" CZ ARG E 365 " ideal model delta sigma weight residual 1.326 1.364 -0.038 1.10e-02 8.26e+03 1.17e+01 bond pdb=" CG MET E 411 " pdb=" SD MET E 411 " ideal model delta sigma weight residual 1.803 1.718 0.085 2.50e-02 1.60e+03 1.16e+01 bond pdb=" NE ARG A 365 " pdb=" CZ ARG A 365 " ideal model delta sigma weight residual 1.326 1.363 -0.037 1.10e-02 8.26e+03 1.16e+01 ... (remaining 15730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 18048 1.79 - 3.59: 2776 3.59 - 5.38: 491 5.38 - 7.17: 93 7.17 - 8.97: 6 Bond angle restraints: 21414 Sorted by residual: angle pdb=" C GLY E 215 " pdb=" N PRO E 216 " pdb=" CA PRO E 216 " ideal model delta sigma weight residual 119.56 128.53 -8.97 1.02e+00 9.61e-01 7.73e+01 angle pdb=" C GLY A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta sigma weight residual 119.56 128.51 -8.95 1.02e+00 9.61e-01 7.70e+01 angle pdb=" C GLY B 215 " pdb=" N PRO B 216 " pdb=" CA PRO B 216 " ideal model delta sigma weight residual 119.56 128.51 -8.95 1.02e+00 9.61e-01 7.70e+01 angle pdb=" N VAL E 75 " pdb=" CA VAL E 75 " pdb=" C VAL E 75 " ideal model delta sigma weight residual 110.42 117.46 -7.04 9.60e-01 1.09e+00 5.37e+01 angle pdb=" N VAL A 75 " pdb=" CA VAL A 75 " pdb=" C VAL A 75 " ideal model delta sigma weight residual 110.42 117.44 -7.02 9.60e-01 1.09e+00 5.35e+01 ... (remaining 21409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 9272 17.36 - 34.72: 286 34.72 - 52.08: 75 52.08 - 69.45: 45 69.45 - 86.81: 15 Dihedral angle restraints: 9693 sinusoidal: 3879 harmonic: 5814 Sorted by residual: dihedral pdb=" CB CYS E 71 " pdb=" SG CYS E 71 " pdb=" SG CYS E 192 " pdb=" CB CYS E 192 " ideal model delta sinusoidal sigma weight residual -86.00 -118.97 32.97 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -118.94 32.94 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" CB CYS B 71 " pdb=" SG CYS B 71 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -118.93 32.93 1 1.00e+01 1.00e-02 1.54e+01 ... (remaining 9690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1784 0.084 - 0.168: 625 0.168 - 0.253: 137 0.253 - 0.337: 35 0.337 - 0.421: 14 Chirality restraints: 2595 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.13e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.10e+02 ... (remaining 2592 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 67 " 0.045 2.00e-02 2.50e+03 4.55e-02 2.59e+01 pdb=" CG ASN E 67 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN E 67 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN E 67 " -0.069 2.00e-02 2.50e+03 pdb=" C1 NAG E 602 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 67 " 0.045 2.00e-02 2.50e+03 4.54e-02 2.58e+01 pdb=" CG ASN A 67 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 67 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 67 " -0.068 2.00e-02 2.50e+03 pdb=" C1 NAG A 602 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 67 " -0.045 2.00e-02 2.50e+03 4.53e-02 2.56e+01 pdb=" CG ASN B 67 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 67 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 67 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG B 602 " -0.055 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 5224 2.86 - 3.37: 14212 3.37 - 3.88: 27455 3.88 - 4.39: 31711 4.39 - 4.90: 53008 Nonbonded interactions: 131610 Sorted by model distance: nonbonded pdb=" OG SER B 50 " pdb=" OG1 THR B 286 " model vdw 2.351 3.040 nonbonded pdb=" OG SER E 50 " pdb=" OG1 THR E 286 " model vdw 2.352 3.040 nonbonded pdb=" OG SER A 50 " pdb=" OG1 THR A 286 " model vdw 2.352 3.040 nonbonded pdb=" CG PRO A 347 " pdb=" O LEU B 367 " model vdw 2.427 3.440 nonbonded pdb=" O LEU A 367 " pdb=" CG PRO E 347 " model vdw 2.427 3.440 ... (remaining 131605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.570 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.014 0.094 15774 Z= 0.734 Angle : 1.389 8.968 21510 Z= 0.929 Chirality : 0.093 0.421 2595 Planarity : 0.006 0.032 2652 Dihedral : 11.169 86.808 5904 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.17 % Allowed : 1.22 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 1962 helix: -0.45 (0.21), residues: 438 sheet: 0.45 (0.21), residues: 528 loop : 0.43 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 365 TYR 0.038 0.005 TYR B 46 PHE 0.023 0.004 PHE D 79 TRP 0.023 0.006 TRP B 308 HIS 0.002 0.001 HIS C 33 Details of bonding type rmsd covalent geometry : bond 0.01373 (15735) covalent geometry : angle 1.37902 (21414) SS BOND : bond 0.02289 ( 21) SS BOND : angle 2.83483 ( 42) hydrogen bonds : bond 0.16286 ( 644) hydrogen bonds : angle 7.72580 ( 1815) link_BETA1-4 : bond 0.05557 ( 6) link_BETA1-4 : angle 2.65973 ( 18) link_NAG-ASN : bond 0.05771 ( 12) link_NAG-ASN : angle 3.01484 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 398 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8086 (ttp-170) cc_final: 0.7848 (ttm-80) REVERT: H 45 LYS cc_start: 0.8261 (tmmt) cc_final: 0.8061 (pmtt) REVERT: B 138 MET cc_start: 0.8075 (mmm) cc_final: 0.7645 (mmm) REVERT: B 155 ASN cc_start: 0.7583 (p0) cc_final: 0.6947 (t0) REVERT: E 138 MET cc_start: 0.7992 (mmm) cc_final: 0.7422 (mmm) REVERT: E 244 ARG cc_start: 0.7921 (ttp-170) cc_final: 0.7721 (ttp-170) REVERT: F 31 TYR cc_start: 0.8598 (m-80) cc_final: 0.8334 (m-80) outliers start: 3 outliers final: 1 residues processed: 401 average time/residue: 0.4521 time to fit residues: 203.6209 Evaluate side-chains 228 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 393 GLN A 395 GLN H 77 ASN B 100 ASN B 127 GLN B 395 GLN D 77 ASN E 100 ASN E 127 GLN E 182 ASN E 194 GLN E 219 GLN E 395 GLN G 77 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.145186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129598 restraints weight = 18042.178| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.26 r_work: 0.3286 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15774 Z= 0.207 Angle : 0.668 9.706 21510 Z= 0.357 Chirality : 0.050 0.363 2595 Planarity : 0.004 0.031 2652 Dihedral : 6.408 54.007 2510 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.38 % Allowed : 9.09 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 1962 helix: 0.58 (0.23), residues: 444 sheet: 0.15 (0.20), residues: 603 loop : 0.24 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 365 TYR 0.020 0.002 TYR E 438 PHE 0.014 0.002 PHE A 212 TRP 0.023 0.002 TRP G 109 HIS 0.004 0.002 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00485 (15735) covalent geometry : angle 0.64849 (21414) SS BOND : bond 0.00274 ( 21) SS BOND : angle 1.64953 ( 42) hydrogen bonds : bond 0.04712 ( 644) hydrogen bonds : angle 5.73838 ( 1815) link_BETA1-4 : bond 0.00629 ( 6) link_BETA1-4 : angle 1.85574 ( 18) link_NAG-ASN : bond 0.00608 ( 12) link_NAG-ASN : angle 3.44717 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 238 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8258 (ptmt) REVERT: A 56 ASP cc_start: 0.7740 (m-30) cc_final: 0.7487 (m-30) REVERT: A 135 TYR cc_start: 0.8721 (t80) cc_final: 0.8328 (t80) REVERT: A 244 ARG cc_start: 0.8625 (ttp-170) cc_final: 0.7925 (ttm-80) REVERT: A 304 ASP cc_start: 0.7046 (t0) cc_final: 0.6807 (t0) REVERT: A 425 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8182 (mp) REVERT: A 453 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6692 (pttp) REVERT: L 31 TYR cc_start: 0.8583 (m-80) cc_final: 0.8372 (m-80) REVERT: B 139 LYS cc_start: 0.7456 (mmmt) cc_final: 0.7184 (mppt) REVERT: B 155 ASN cc_start: 0.8111 (p0) cc_final: 0.7118 (t0) REVERT: B 156 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7697 (tp30) REVERT: B 220 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: B 306 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8520 (t) REVERT: C 31 TYR cc_start: 0.8523 (m-80) cc_final: 0.8284 (m-80) REVERT: C 102 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7834 (ttpt) REVERT: D 45 LYS cc_start: 0.8644 (tmtm) cc_final: 0.7971 (ptpp) REVERT: E 32 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8380 (mttp) REVERT: E 138 MET cc_start: 0.8091 (mmm) cc_final: 0.7678 (mmm) REVERT: E 166 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: E 220 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7723 (t0) REVERT: E 244 ARG cc_start: 0.8487 (ttp-170) cc_final: 0.7633 (tpp-160) REVERT: F 11 MET cc_start: 0.7295 (mtp) cc_final: 0.6820 (ttm) REVERT: F 44 LYS cc_start: 0.8137 (tttt) cc_final: 0.7884 (ttpp) REVERT: F 74 ILE cc_start: 0.8274 (mt) cc_final: 0.7817 (mt) REVERT: F 86 TYR cc_start: 0.9020 (m-80) cc_final: 0.8744 (m-80) REVERT: G 45 LYS cc_start: 0.8054 (ptpp) cc_final: 0.7738 (ptmm) REVERT: G 73 ASP cc_start: 0.7743 (t0) cc_final: 0.7216 (t70) outliers start: 58 outliers final: 22 residues processed: 277 average time/residue: 0.4608 time to fit residues: 143.2294 Evaluate side-chains 239 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN L 52 ASN H 77 ASN B 194 GLN B 393 GLN C 52 ASN D 77 ASN E 194 GLN F 52 ASN G 77 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.141705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.126377 restraints weight = 18240.275| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.17 r_work: 0.3257 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15774 Z= 0.216 Angle : 0.643 7.722 21510 Z= 0.338 Chirality : 0.049 0.304 2595 Planarity : 0.004 0.034 2652 Dihedral : 6.071 50.221 2508 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.97 % Allowed : 11.31 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 1962 helix: 0.78 (0.23), residues: 450 sheet: -0.08 (0.20), residues: 600 loop : 0.03 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 365 TYR 0.016 0.002 TYR E 438 PHE 0.018 0.002 PHE A 212 TRP 0.020 0.002 TRP G 109 HIS 0.007 0.002 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00513 (15735) covalent geometry : angle 0.62805 (21414) SS BOND : bond 0.00542 ( 21) SS BOND : angle 1.96078 ( 42) hydrogen bonds : bond 0.04218 ( 644) hydrogen bonds : angle 5.43908 ( 1815) link_BETA1-4 : bond 0.00603 ( 6) link_BETA1-4 : angle 1.62505 ( 18) link_NAG-ASN : bond 0.00340 ( 12) link_NAG-ASN : angle 2.50338 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7949 (m-40) cc_final: 0.7571 (t160) REVERT: A 135 TYR cc_start: 0.8751 (t80) cc_final: 0.8355 (t80) REVERT: A 220 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7612 (t0) REVERT: A 244 ARG cc_start: 0.8553 (ttp-170) cc_final: 0.7942 (ttm-80) REVERT: A 304 ASP cc_start: 0.7232 (t0) cc_final: 0.6845 (t0) REVERT: A 425 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8278 (mp) REVERT: A 453 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6766 (pttp) REVERT: B 49 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8671 (pttp) REVERT: B 139 LYS cc_start: 0.7558 (mmmt) cc_final: 0.7291 (mppt) REVERT: B 155 ASN cc_start: 0.8136 (p0) cc_final: 0.7181 (t0) REVERT: B 156 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7754 (tp30) REVERT: B 161 LEU cc_start: 0.9036 (mt) cc_final: 0.8757 (mp) REVERT: B 220 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: B 304 ASP cc_start: 0.7092 (t0) cc_final: 0.6884 (t0) REVERT: B 306 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8514 (t) REVERT: B 390 VAL cc_start: 0.8420 (m) cc_final: 0.8024 (p) REVERT: C 31 TYR cc_start: 0.8558 (m-80) cc_final: 0.8285 (m-80) REVERT: C 71 SER cc_start: 0.8714 (p) cc_final: 0.8377 (t) REVERT: C 102 LYS cc_start: 0.8249 (ttmm) cc_final: 0.7834 (ttpt) REVERT: D 45 LYS cc_start: 0.8565 (tmtm) cc_final: 0.7941 (ptpp) REVERT: D 113 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8321 (p) REVERT: E 32 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8423 (mttp) REVERT: E 76 MET cc_start: 0.8838 (mmm) cc_final: 0.8605 (mmm) REVERT: E 138 MET cc_start: 0.8107 (mmm) cc_final: 0.7747 (mmm) REVERT: E 139 LYS cc_start: 0.7889 (mppt) cc_final: 0.7663 (mppt) REVERT: E 220 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7901 (t0) REVERT: E 244 ARG cc_start: 0.8468 (ttp-170) cc_final: 0.7762 (ttp-170) REVERT: E 304 ASP cc_start: 0.7061 (t0) cc_final: 0.6799 (t0) REVERT: F 44 LYS cc_start: 0.8252 (tttt) cc_final: 0.7786 (ptpp) REVERT: F 74 ILE cc_start: 0.8341 (mt) cc_final: 0.7861 (mt) REVERT: F 86 TYR cc_start: 0.9044 (m-80) cc_final: 0.8810 (m-80) outliers start: 51 outliers final: 27 residues processed: 263 average time/residue: 0.4722 time to fit residues: 139.6242 Evaluate side-chains 252 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 393 GLN D 77 ASN E 162 GLN E 393 GLN G 77 ASN G 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.127944 restraints weight = 18487.843| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.15 r_work: 0.3266 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15774 Z= 0.174 Angle : 0.575 7.236 21510 Z= 0.302 Chirality : 0.047 0.325 2595 Planarity : 0.004 0.039 2652 Dihedral : 5.777 50.535 2508 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.44 % Allowed : 11.60 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1962 helix: 0.97 (0.24), residues: 450 sheet: -0.12 (0.20), residues: 597 loop : -0.01 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 365 TYR 0.014 0.002 TYR E 438 PHE 0.024 0.002 PHE A 212 TRP 0.017 0.002 TRP G 35 HIS 0.004 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00413 (15735) covalent geometry : angle 0.56633 (21414) SS BOND : bond 0.00382 ( 21) SS BOND : angle 1.11693 ( 42) hydrogen bonds : bond 0.03693 ( 644) hydrogen bonds : angle 5.22796 ( 1815) link_BETA1-4 : bond 0.00542 ( 6) link_BETA1-4 : angle 1.65531 ( 18) link_NAG-ASN : bond 0.00408 ( 12) link_NAG-ASN : angle 1.96599 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8418 (ptpp) REVERT: A 115 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7879 (mmm) REVERT: A 135 TYR cc_start: 0.8720 (t80) cc_final: 0.8304 (t80) REVERT: A 220 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7780 (t0) REVERT: A 244 ARG cc_start: 0.8528 (ttp-170) cc_final: 0.7715 (tpp-160) REVERT: A 304 ASP cc_start: 0.7013 (t0) cc_final: 0.6598 (t0) REVERT: A 390 VAL cc_start: 0.8310 (m) cc_final: 0.7907 (p) REVERT: A 425 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8308 (mp) REVERT: A 453 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6839 (pttp) REVERT: B 139 LYS cc_start: 0.7574 (mmmt) cc_final: 0.7291 (mppt) REVERT: B 155 ASN cc_start: 0.8034 (p0) cc_final: 0.7104 (t0) REVERT: B 156 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: B 161 LEU cc_start: 0.8950 (mt) cc_final: 0.8655 (mp) REVERT: B 212 PHE cc_start: 0.7693 (t80) cc_final: 0.7436 (t80) REVERT: B 220 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7678 (t0) REVERT: B 304 ASP cc_start: 0.7123 (t0) cc_final: 0.6900 (t0) REVERT: B 306 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8478 (t) REVERT: B 390 VAL cc_start: 0.8315 (m) cc_final: 0.7922 (p) REVERT: C 31 TYR cc_start: 0.8559 (m-80) cc_final: 0.8250 (m-80) REVERT: C 71 SER cc_start: 0.8760 (p) cc_final: 0.8473 (t) REVERT: C 102 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7847 (ttpt) REVERT: D 45 LYS cc_start: 0.8550 (tmtm) cc_final: 0.8213 (ptpp) REVERT: E 32 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8403 (mttp) REVERT: E 138 MET cc_start: 0.8073 (mmm) cc_final: 0.7703 (mmm) REVERT: E 139 LYS cc_start: 0.7878 (mppt) cc_final: 0.7631 (mppt) REVERT: E 186 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.8072 (p) REVERT: E 220 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7886 (t0) REVERT: E 244 ARG cc_start: 0.8479 (ttp-170) cc_final: 0.7713 (ttp-170) REVERT: E 304 ASP cc_start: 0.7203 (t0) cc_final: 0.6898 (t0) REVERT: E 411 MET cc_start: 0.8608 (tmm) cc_final: 0.8276 (tmm) REVERT: E 427 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8121 (mt) REVERT: F 44 LYS cc_start: 0.8237 (tttt) cc_final: 0.7714 (ptpp) REVERT: F 74 ILE cc_start: 0.8380 (mt) cc_final: 0.7929 (mt) REVERT: F 86 TYR cc_start: 0.9000 (m-80) cc_final: 0.8746 (m-80) REVERT: G 45 LYS cc_start: 0.7926 (ptpp) cc_final: 0.7716 (ptmt) outliers start: 59 outliers final: 32 residues processed: 282 average time/residue: 0.4345 time to fit residues: 138.0142 Evaluate side-chains 266 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 121 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 0.0570 chunk 182 optimal weight: 0.3980 chunk 172 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 393 GLN H 16 GLN H 77 ASN B 325 ASN B 393 GLN D 77 ASN G 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.144537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.128856 restraints weight = 18311.092| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.27 r_work: 0.3282 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15774 Z= 0.131 Angle : 0.559 10.399 21510 Z= 0.292 Chirality : 0.048 0.514 2595 Planarity : 0.004 0.040 2652 Dihedral : 5.549 50.231 2508 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.67 % Allowed : 11.95 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1962 helix: 1.25 (0.25), residues: 444 sheet: -0.10 (0.21), residues: 597 loop : 0.03 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.012 0.001 TYR E 281 PHE 0.025 0.002 PHE A 212 TRP 0.015 0.001 TRP G 35 HIS 0.002 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00300 (15735) covalent geometry : angle 0.53542 (21414) SS BOND : bond 0.00189 ( 21) SS BOND : angle 2.74546 ( 42) hydrogen bonds : bond 0.03324 ( 644) hydrogen bonds : angle 5.04375 ( 1815) link_BETA1-4 : bond 0.00584 ( 6) link_BETA1-4 : angle 1.64700 ( 18) link_NAG-ASN : bond 0.00543 ( 12) link_NAG-ASN : angle 2.45211 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 253 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8534 (ptpp) REVERT: A 115 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7872 (mmm) REVERT: A 135 TYR cc_start: 0.8692 (t80) cc_final: 0.8270 (t80) REVERT: A 155 ASN cc_start: 0.8115 (p0) cc_final: 0.7102 (t0) REVERT: A 220 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7762 (t0) REVERT: A 244 ARG cc_start: 0.8462 (ttp-170) cc_final: 0.7635 (tpp-160) REVERT: A 304 ASP cc_start: 0.7136 (t0) cc_final: 0.6703 (t0) REVERT: A 390 VAL cc_start: 0.8268 (m) cc_final: 0.7931 (p) REVERT: A 425 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8241 (mp) REVERT: A 453 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.6894 (pttp) REVERT: B 139 LYS cc_start: 0.7555 (mmmt) cc_final: 0.7276 (mppt) REVERT: B 155 ASN cc_start: 0.8013 (p0) cc_final: 0.7136 (t0) REVERT: B 156 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7660 (tp30) REVERT: B 161 LEU cc_start: 0.8919 (mt) cc_final: 0.8607 (mp) REVERT: B 212 PHE cc_start: 0.7709 (t80) cc_final: 0.7444 (t80) REVERT: B 220 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7752 (t0) REVERT: B 244 ARG cc_start: 0.8050 (ttm-80) cc_final: 0.7190 (ttt180) REVERT: B 258 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: B 304 ASP cc_start: 0.7087 (t0) cc_final: 0.6871 (t0) REVERT: B 390 VAL cc_start: 0.8312 (m) cc_final: 0.7953 (p) REVERT: C 31 TYR cc_start: 0.8486 (m-80) cc_final: 0.8168 (m-80) REVERT: C 71 SER cc_start: 0.8638 (p) cc_final: 0.8387 (t) REVERT: C 102 LYS cc_start: 0.8254 (ttmm) cc_final: 0.7841 (ttpt) REVERT: D 45 LYS cc_start: 0.8477 (tmtm) cc_final: 0.8214 (ptpp) REVERT: E 32 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8365 (mttp) REVERT: E 138 MET cc_start: 0.8062 (mmm) cc_final: 0.7677 (mmm) REVERT: E 139 LYS cc_start: 0.7895 (mppt) cc_final: 0.7653 (mppt) REVERT: E 220 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7970 (t0) REVERT: E 244 ARG cc_start: 0.8450 (ttp-170) cc_final: 0.7695 (ttp-170) REVERT: E 304 ASP cc_start: 0.7266 (t0) cc_final: 0.6934 (t0) REVERT: E 411 MET cc_start: 0.8615 (tmm) cc_final: 0.8305 (tmm) REVERT: F 44 LYS cc_start: 0.8241 (tttt) cc_final: 0.7739 (ptpp) REVERT: F 74 ILE cc_start: 0.8348 (mt) cc_final: 0.7874 (mt) REVERT: F 86 TYR cc_start: 0.8949 (m-80) cc_final: 0.8709 (m-80) REVERT: G 45 LYS cc_start: 0.7902 (ptpp) cc_final: 0.7701 (ptmt) outliers start: 63 outliers final: 31 residues processed: 292 average time/residue: 0.4461 time to fit residues: 147.0448 Evaluate side-chains 275 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 45 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 178 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 186 optimal weight: 0.4980 chunk 159 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN H 16 GLN B 162 GLN D 77 ASN G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.142745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.127424 restraints weight = 18141.462| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.18 r_work: 0.3273 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15774 Z= 0.161 Angle : 0.579 10.809 21510 Z= 0.302 Chirality : 0.048 0.462 2595 Planarity : 0.004 0.041 2652 Dihedral : 5.492 50.267 2508 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.08 % Allowed : 11.83 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.19), residues: 1962 helix: 1.24 (0.25), residues: 444 sheet: -0.14 (0.21), residues: 600 loop : -0.03 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 365 TYR 0.013 0.001 TYR D 51 PHE 0.016 0.002 PHE H 79 TRP 0.015 0.002 TRP G 35 HIS 0.003 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00377 (15735) covalent geometry : angle 0.55410 (21414) SS BOND : bond 0.00353 ( 21) SS BOND : angle 2.96795 ( 42) hydrogen bonds : bond 0.03483 ( 644) hydrogen bonds : angle 5.07634 ( 1815) link_BETA1-4 : bond 0.00535 ( 6) link_BETA1-4 : angle 1.70386 ( 18) link_NAG-ASN : bond 0.00701 ( 12) link_NAG-ASN : angle 2.46142 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 238 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8446 (ptpp) REVERT: A 115 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7871 (mmm) REVERT: A 135 TYR cc_start: 0.8679 (t80) cc_final: 0.8234 (t80) REVERT: A 155 ASN cc_start: 0.8121 (p0) cc_final: 0.7151 (t0) REVERT: A 220 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7786 (t0) REVERT: A 244 ARG cc_start: 0.8448 (ttp-170) cc_final: 0.7672 (tpp-160) REVERT: A 304 ASP cc_start: 0.7158 (t0) cc_final: 0.6724 (t0) REVERT: A 390 VAL cc_start: 0.8317 (m) cc_final: 0.7964 (p) REVERT: A 425 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8323 (mp) REVERT: A 453 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6848 (pttp) REVERT: H 16 GLN cc_start: 0.7590 (mt0) cc_final: 0.7359 (mt0) REVERT: B 139 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7318 (mppt) REVERT: B 155 ASN cc_start: 0.8009 (p0) cc_final: 0.7194 (t0) REVERT: B 156 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7576 (tp30) REVERT: B 161 LEU cc_start: 0.8903 (mt) cc_final: 0.8606 (mp) REVERT: B 212 PHE cc_start: 0.7695 (t80) cc_final: 0.7417 (t80) REVERT: B 220 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7709 (t70) REVERT: B 244 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7168 (ttt180) REVERT: B 258 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: B 304 ASP cc_start: 0.7010 (t0) cc_final: 0.6801 (t0) REVERT: B 390 VAL cc_start: 0.8298 (m) cc_final: 0.7900 (p) REVERT: C 31 TYR cc_start: 0.8551 (m-80) cc_final: 0.8209 (m-80) REVERT: C 71 SER cc_start: 0.8627 (p) cc_final: 0.8381 (t) REVERT: C 102 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7884 (ttpt) REVERT: D 4 LEU cc_start: 0.9099 (mp) cc_final: 0.8881 (mp) REVERT: D 45 LYS cc_start: 0.8435 (tmtm) cc_final: 0.8179 (ptpp) REVERT: E 32 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8375 (mttp) REVERT: E 76 MET cc_start: 0.8704 (mmm) cc_final: 0.8433 (mmm) REVERT: E 138 MET cc_start: 0.8087 (mmm) cc_final: 0.7678 (mmm) REVERT: E 139 LYS cc_start: 0.7884 (mppt) cc_final: 0.7637 (mppt) REVERT: E 220 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7975 (t0) REVERT: E 244 ARG cc_start: 0.8436 (ttp-170) cc_final: 0.7713 (ttp-170) REVERT: E 304 ASP cc_start: 0.7278 (t0) cc_final: 0.6953 (t0) REVERT: E 329 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8171 (ptpt) REVERT: E 411 MET cc_start: 0.8631 (tmm) cc_final: 0.8335 (tmm) REVERT: F 44 LYS cc_start: 0.8240 (tttt) cc_final: 0.7754 (ptpp) REVERT: F 74 ILE cc_start: 0.8338 (mt) cc_final: 0.7911 (mt) REVERT: F 86 TYR cc_start: 0.9002 (m-80) cc_final: 0.8761 (m-80) REVERT: G 45 LYS cc_start: 0.7909 (ptpp) cc_final: 0.7691 (ptmt) outliers start: 70 outliers final: 48 residues processed: 280 average time/residue: 0.4767 time to fit residues: 149.4462 Evaluate side-chains 289 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 230 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN H 77 ASN B 189 GLN D 77 ASN E 393 GLN G 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.141789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.126972 restraints weight = 18513.765| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.14 r_work: 0.3252 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15774 Z= 0.209 Angle : 0.610 9.915 21510 Z= 0.317 Chirality : 0.049 0.412 2595 Planarity : 0.004 0.044 2652 Dihedral : 5.660 50.500 2508 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.14 % Allowed : 12.12 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 1962 helix: 1.00 (0.25), residues: 450 sheet: -0.14 (0.21), residues: 585 loop : -0.23 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 365 TYR 0.015 0.002 TYR D 51 PHE 0.026 0.002 PHE A 212 TRP 0.015 0.002 TRP G 35 HIS 0.004 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00499 (15735) covalent geometry : angle 0.59138 (21414) SS BOND : bond 0.00336 ( 21) SS BOND : angle 2.48059 ( 42) hydrogen bonds : bond 0.03773 ( 644) hydrogen bonds : angle 5.17489 ( 1815) link_BETA1-4 : bond 0.00522 ( 6) link_BETA1-4 : angle 1.79734 ( 18) link_NAG-ASN : bond 0.00604 ( 12) link_NAG-ASN : angle 2.35249 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 229 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8416 (ptpp) REVERT: A 115 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7889 (mmm) REVERT: A 135 TYR cc_start: 0.8687 (t80) cc_final: 0.8277 (t80) REVERT: A 155 ASN cc_start: 0.8093 (p0) cc_final: 0.7201 (t0) REVERT: A 220 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7864 (t0) REVERT: A 244 ARG cc_start: 0.8460 (ttp-170) cc_final: 0.7693 (tpp-160) REVERT: A 304 ASP cc_start: 0.7184 (t0) cc_final: 0.6765 (t0) REVERT: A 390 VAL cc_start: 0.8310 (m) cc_final: 0.7917 (p) REVERT: A 425 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8385 (mp) REVERT: A 453 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.6868 (pttp) REVERT: B 139 LYS cc_start: 0.7650 (mmmt) cc_final: 0.7357 (mppt) REVERT: B 155 ASN cc_start: 0.8033 (p0) cc_final: 0.7210 (t0) REVERT: B 156 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: B 161 LEU cc_start: 0.8890 (mt) cc_final: 0.8606 (mp) REVERT: B 212 PHE cc_start: 0.7710 (t80) cc_final: 0.7405 (t80) REVERT: B 220 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7696 (t70) REVERT: B 244 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7183 (ttt180) REVERT: B 258 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: B 304 ASP cc_start: 0.7031 (t0) cc_final: 0.6822 (t0) REVERT: C 71 SER cc_start: 0.8654 (p) cc_final: 0.8390 (t) REVERT: C 102 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7904 (ttpt) REVERT: D 29 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7153 (tp) REVERT: D 45 LYS cc_start: 0.8490 (tmtm) cc_final: 0.8219 (ptpp) REVERT: E 32 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8413 (mttp) REVERT: E 76 MET cc_start: 0.8739 (mmm) cc_final: 0.8502 (mmm) REVERT: E 138 MET cc_start: 0.8020 (mmm) cc_final: 0.7396 (mmm) REVERT: E 139 LYS cc_start: 0.7870 (mppt) cc_final: 0.7627 (mppt) REVERT: E 220 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7989 (t0) REVERT: E 244 ARG cc_start: 0.8486 (ttp-170) cc_final: 0.7740 (ttp-170) REVERT: E 304 ASP cc_start: 0.7291 (t0) cc_final: 0.6983 (t0) REVERT: E 329 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8215 (ptpt) REVERT: E 411 MET cc_start: 0.8676 (tmm) cc_final: 0.8388 (tmm) REVERT: F 44 LYS cc_start: 0.8291 (tttt) cc_final: 0.7766 (ptpp) REVERT: F 74 ILE cc_start: 0.8400 (mt) cc_final: 0.7939 (mt) REVERT: F 86 TYR cc_start: 0.9045 (m-80) cc_final: 0.8804 (m-80) REVERT: G 45 LYS cc_start: 0.7984 (ptpp) cc_final: 0.7745 (ptmm) outliers start: 71 outliers final: 48 residues processed: 274 average time/residue: 0.4644 time to fit residues: 142.7473 Evaluate side-chains 288 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 228 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 50 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 151 optimal weight: 0.2980 chunk 117 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 165 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN H 16 GLN B 189 GLN B 393 GLN D 77 ASN E 393 GLN G 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.143620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.128329 restraints weight = 18348.932| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.19 r_work: 0.3276 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15774 Z= 0.145 Angle : 0.548 10.575 21510 Z= 0.286 Chirality : 0.047 0.397 2595 Planarity : 0.004 0.044 2652 Dihedral : 5.465 50.455 2508 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.67 % Allowed : 12.30 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 1962 helix: 1.15 (0.25), residues: 450 sheet: -0.15 (0.21), residues: 579 loop : -0.17 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 365 TYR 0.012 0.001 TYR G 51 PHE 0.026 0.002 PHE A 212 TRP 0.016 0.001 TRP G 35 HIS 0.002 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00340 (15735) covalent geometry : angle 0.53105 (21414) SS BOND : bond 0.00202 ( 21) SS BOND : angle 2.20478 ( 42) hydrogen bonds : bond 0.03363 ( 644) hydrogen bonds : angle 5.01208 ( 1815) link_BETA1-4 : bond 0.00506 ( 6) link_BETA1-4 : angle 1.64754 ( 18) link_NAG-ASN : bond 0.00513 ( 12) link_NAG-ASN : angle 2.20422 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 241 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8482 (ptpp) REVERT: A 115 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7909 (mmm) REVERT: A 135 TYR cc_start: 0.8703 (t80) cc_final: 0.8270 (t80) REVERT: A 155 ASN cc_start: 0.8086 (p0) cc_final: 0.7190 (t0) REVERT: A 220 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7791 (t0) REVERT: A 244 ARG cc_start: 0.8398 (ttp-170) cc_final: 0.7654 (tpp-160) REVERT: A 304 ASP cc_start: 0.7191 (t0) cc_final: 0.6791 (t0) REVERT: A 390 VAL cc_start: 0.8342 (m) cc_final: 0.7988 (p) REVERT: A 416 THR cc_start: 0.8072 (t) cc_final: 0.7666 (t) REVERT: A 425 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 453 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.6864 (pttp) REVERT: B 139 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7324 (mppt) REVERT: B 155 ASN cc_start: 0.8020 (p0) cc_final: 0.7196 (t0) REVERT: B 156 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: B 161 LEU cc_start: 0.8878 (mt) cc_final: 0.8589 (mp) REVERT: B 212 PHE cc_start: 0.7668 (t80) cc_final: 0.7371 (t80) REVERT: B 220 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7777 (t70) REVERT: B 244 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7171 (ttt180) REVERT: B 258 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: B 304 ASP cc_start: 0.7007 (t0) cc_final: 0.6767 (t0) REVERT: B 390 VAL cc_start: 0.8093 (m) cc_final: 0.7731 (p) REVERT: C 71 SER cc_start: 0.8603 (p) cc_final: 0.8377 (t) REVERT: C 102 LYS cc_start: 0.8311 (ttmm) cc_final: 0.7906 (ttpt) REVERT: C 106 LYS cc_start: 0.7195 (mtmt) cc_final: 0.6986 (mtpt) REVERT: D 45 LYS cc_start: 0.8407 (tmtm) cc_final: 0.8149 (ptpp) REVERT: E 32 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8399 (mttp) REVERT: E 76 MET cc_start: 0.8727 (mmm) cc_final: 0.8467 (mmm) REVERT: E 138 MET cc_start: 0.8036 (mmm) cc_final: 0.7432 (mmm) REVERT: E 139 LYS cc_start: 0.7858 (mppt) cc_final: 0.7622 (mppt) REVERT: E 220 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7963 (t0) REVERT: E 244 ARG cc_start: 0.8414 (ttp-170) cc_final: 0.7680 (ttp-170) REVERT: E 304 ASP cc_start: 0.7235 (t0) cc_final: 0.6940 (t0) REVERT: E 329 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8207 (ptpt) REVERT: E 411 MET cc_start: 0.8649 (tmm) cc_final: 0.8365 (tmm) REVERT: F 44 LYS cc_start: 0.8255 (tttt) cc_final: 0.7741 (ptpp) REVERT: F 74 ILE cc_start: 0.8398 (mt) cc_final: 0.7964 (mt) REVERT: F 86 TYR cc_start: 0.9007 (m-80) cc_final: 0.8771 (m-80) REVERT: G 45 LYS cc_start: 0.7960 (ptpp) cc_final: 0.7731 (ptmt) outliers start: 63 outliers final: 44 residues processed: 280 average time/residue: 0.4748 time to fit residues: 149.2896 Evaluate side-chains 289 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 159 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN H 16 GLN H 77 ASN B 189 GLN D 77 ASN E 393 GLN G 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.129709 restraints weight = 18102.870| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.19 r_work: 0.3292 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15774 Z= 0.119 Angle : 0.520 9.644 21510 Z= 0.272 Chirality : 0.046 0.372 2595 Planarity : 0.004 0.041 2652 Dihedral : 5.312 50.284 2508 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.50 % Allowed : 13.11 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1962 helix: 1.21 (0.25), residues: 456 sheet: -0.15 (0.21), residues: 579 loop : -0.10 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.012 0.001 TYR G 51 PHE 0.031 0.001 PHE A 212 TRP 0.016 0.001 TRP G 35 HIS 0.002 0.001 HIS E 29 Details of bonding type rmsd covalent geometry : bond 0.00275 (15735) covalent geometry : angle 0.50573 (21414) SS BOND : bond 0.00166 ( 21) SS BOND : angle 1.93083 ( 42) hydrogen bonds : bond 0.03161 ( 644) hydrogen bonds : angle 4.90706 ( 1815) link_BETA1-4 : bond 0.00521 ( 6) link_BETA1-4 : angle 1.54395 ( 18) link_NAG-ASN : bond 0.00458 ( 12) link_NAG-ASN : angle 2.03734 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 246 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8554 (ptpp) REVERT: A 115 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7893 (mmm) REVERT: A 135 TYR cc_start: 0.8667 (t80) cc_final: 0.8287 (t80) REVERT: A 155 ASN cc_start: 0.7994 (p0) cc_final: 0.7100 (t0) REVERT: A 220 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7927 (t0) REVERT: A 244 ARG cc_start: 0.8388 (ttp-170) cc_final: 0.7595 (tpp-160) REVERT: A 304 ASP cc_start: 0.7090 (t0) cc_final: 0.6729 (t0) REVERT: A 390 VAL cc_start: 0.8321 (m) cc_final: 0.7976 (p) REVERT: A 416 THR cc_start: 0.8019 (t) cc_final: 0.7620 (t) REVERT: A 425 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8339 (mp) REVERT: A 453 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.6851 (pttp) REVERT: B 139 LYS cc_start: 0.7622 (mmmt) cc_final: 0.7312 (mppt) REVERT: B 155 ASN cc_start: 0.7981 (p0) cc_final: 0.7179 (t0) REVERT: B 156 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: B 161 LEU cc_start: 0.8807 (mt) cc_final: 0.8521 (mp) REVERT: B 212 PHE cc_start: 0.7619 (t80) cc_final: 0.7390 (t80) REVERT: B 220 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7820 (t0) REVERT: B 244 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7163 (ttt180) REVERT: B 258 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: B 304 ASP cc_start: 0.7023 (t0) cc_final: 0.6757 (t0) REVERT: B 390 VAL cc_start: 0.7985 (m) cc_final: 0.7678 (p) REVERT: C 17 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6856 (pt0) REVERT: C 102 LYS cc_start: 0.8243 (ttmm) cc_final: 0.7892 (ttpt) REVERT: D 45 LYS cc_start: 0.8417 (tmtm) cc_final: 0.8165 (ptpp) REVERT: E 76 MET cc_start: 0.8739 (mmm) cc_final: 0.8494 (mmm) REVERT: E 138 MET cc_start: 0.8036 (mmm) cc_final: 0.7421 (mmm) REVERT: E 139 LYS cc_start: 0.7840 (mppt) cc_final: 0.7612 (mppt) REVERT: E 155 ASN cc_start: 0.7923 (p0) cc_final: 0.7080 (t0) REVERT: E 220 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7989 (t0) REVERT: E 244 ARG cc_start: 0.8352 (ttp-170) cc_final: 0.7621 (ttp-170) REVERT: E 304 ASP cc_start: 0.7240 (t0) cc_final: 0.7025 (t0) REVERT: E 329 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8181 (ptpt) REVERT: E 411 MET cc_start: 0.8599 (tmm) cc_final: 0.8230 (tmm) REVERT: F 44 LYS cc_start: 0.8252 (tttt) cc_final: 0.7745 (ptpp) REVERT: F 74 ILE cc_start: 0.8335 (mt) cc_final: 0.7895 (mt) REVERT: F 86 TYR cc_start: 0.8958 (m-80) cc_final: 0.8724 (m-80) outliers start: 60 outliers final: 39 residues processed: 283 average time/residue: 0.4534 time to fit residues: 144.3441 Evaluate side-chains 286 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 135 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 87 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN H 16 GLN D 77 ASN E 393 GLN G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.144483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.125695 restraints weight = 18481.609| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.50 r_work: 0.3277 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15774 Z= 0.155 Angle : 0.568 12.672 21510 Z= 0.293 Chirality : 0.049 0.825 2595 Planarity : 0.004 0.040 2652 Dihedral : 5.482 50.524 2508 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.97 % Allowed : 13.93 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 1962 helix: 1.16 (0.25), residues: 456 sheet: -0.16 (0.21), residues: 579 loop : -0.14 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.015 0.001 TYR E 135 PHE 0.016 0.002 PHE H 79 TRP 0.015 0.001 TRP G 35 HIS 0.004 0.001 HIS E 29 Details of bonding type rmsd covalent geometry : bond 0.00368 (15735) covalent geometry : angle 0.54651 (21414) SS BOND : bond 0.00207 ( 21) SS BOND : angle 1.85897 ( 42) hydrogen bonds : bond 0.03388 ( 644) hydrogen bonds : angle 4.98891 ( 1815) link_BETA1-4 : bond 0.00498 ( 6) link_BETA1-4 : angle 1.58415 ( 18) link_NAG-ASN : bond 0.00380 ( 12) link_NAG-ASN : angle 3.13563 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8567 (ptpp) REVERT: A 115 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7924 (mmm) REVERT: A 135 TYR cc_start: 0.8660 (t80) cc_final: 0.8262 (t80) REVERT: A 155 ASN cc_start: 0.8078 (p0) cc_final: 0.7164 (t0) REVERT: A 220 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7892 (t0) REVERT: A 244 ARG cc_start: 0.8474 (ttp-170) cc_final: 0.7718 (tpp-160) REVERT: A 304 ASP cc_start: 0.7337 (t0) cc_final: 0.6938 (t0) REVERT: A 390 VAL cc_start: 0.8379 (m) cc_final: 0.8011 (p) REVERT: A 416 THR cc_start: 0.8080 (t) cc_final: 0.7692 (t) REVERT: A 425 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8491 (mp) REVERT: A 453 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6838 (pttp) REVERT: H 77 ASN cc_start: 0.7706 (t0) cc_final: 0.7126 (t0) REVERT: B 139 LYS cc_start: 0.7684 (mmmt) cc_final: 0.7375 (mppt) REVERT: B 155 ASN cc_start: 0.8095 (p0) cc_final: 0.7259 (t0) REVERT: B 156 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7722 (tp30) REVERT: B 161 LEU cc_start: 0.8851 (mt) cc_final: 0.8559 (mp) REVERT: B 212 PHE cc_start: 0.7812 (t80) cc_final: 0.7471 (t80) REVERT: B 220 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7825 (t70) REVERT: B 244 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7273 (ttt180) REVERT: B 258 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: B 304 ASP cc_start: 0.7169 (t0) cc_final: 0.6890 (t0) REVERT: B 390 VAL cc_start: 0.7938 (m) cc_final: 0.7595 (p) REVERT: C 17 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6921 (pt0) REVERT: C 102 LYS cc_start: 0.8345 (ttmm) cc_final: 0.7917 (ttpt) REVERT: D 45 LYS cc_start: 0.8387 (tmtm) cc_final: 0.8114 (ptpp) REVERT: E 76 MET cc_start: 0.8767 (mmm) cc_final: 0.8530 (mmm) REVERT: E 138 MET cc_start: 0.8102 (mmm) cc_final: 0.7489 (mmm) REVERT: E 139 LYS cc_start: 0.7892 (mppt) cc_final: 0.7656 (mppt) REVERT: E 155 ASN cc_start: 0.8004 (p0) cc_final: 0.7183 (t0) REVERT: E 220 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8027 (t0) REVERT: E 244 ARG cc_start: 0.8451 (ttp-170) cc_final: 0.7689 (ttp-170) REVERT: E 304 ASP cc_start: 0.7439 (t0) cc_final: 0.7181 (t0) REVERT: E 329 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8241 (ptpt) REVERT: E 411 MET cc_start: 0.8688 (tmm) cc_final: 0.8393 (tmm) REVERT: F 44 LYS cc_start: 0.8391 (tttt) cc_final: 0.7847 (ptpp) REVERT: F 74 ILE cc_start: 0.8401 (mt) cc_final: 0.7952 (mt) REVERT: F 86 TYR cc_start: 0.9009 (m-80) cc_final: 0.8757 (m-80) outliers start: 51 outliers final: 38 residues processed: 273 average time/residue: 0.4710 time to fit residues: 144.3512 Evaluate side-chains 282 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 0.0770 chunk 140 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN H 16 GLN B 189 GLN B 289 GLN D 77 ASN E 194 GLN E 393 GLN G 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.126080 restraints weight = 18273.549| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.49 r_work: 0.3281 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15774 Z= 0.146 Angle : 0.553 10.336 21510 Z= 0.287 Chirality : 0.048 0.671 2595 Planarity : 0.004 0.041 2652 Dihedral : 5.486 50.547 2508 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.21 % Allowed : 13.81 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 1962 helix: 1.18 (0.25), residues: 456 sheet: -0.15 (0.21), residues: 579 loop : -0.16 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.014 0.001 TYR E 135 PHE 0.028 0.002 PHE A 212 TRP 0.016 0.001 TRP G 35 HIS 0.003 0.001 HIS E 29 Details of bonding type rmsd covalent geometry : bond 0.00345 (15735) covalent geometry : angle 0.53379 (21414) SS BOND : bond 0.00195 ( 21) SS BOND : angle 1.76175 ( 42) hydrogen bonds : bond 0.03321 ( 644) hydrogen bonds : angle 4.96610 ( 1815) link_BETA1-4 : bond 0.00494 ( 6) link_BETA1-4 : angle 1.56411 ( 18) link_NAG-ASN : bond 0.00467 ( 12) link_NAG-ASN : angle 2.90397 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4720.10 seconds wall clock time: 81 minutes 25.83 seconds (4885.83 seconds total)