Starting phenix.real_space_refine on Mon Jul 6 20:53:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gwa_34307/07_2026/8gwa_34307.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwa_34307/07_2026/8gwa_34307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8gwa_34307/07_2026/8gwa_34307.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gwa_34307/07_2026/8gwa_34307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gwa_34307/07_2026/8gwa_34307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwa_34307/07_2026/8gwa_34307.map" model { file = "/net/cci-nas-00/data/ceres_data/8gwa_34307/07_2026/8gwa_34307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwa_34307/07_2026/8gwa_34307.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 12 7.16 5 P 15 5.49 5 Mg 79 5.21 5 S 139 5.16 5 C 25342 2.51 5 N 5745 2.21 5 O 6326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37660 Number of models: 1 Model: "" Number of chains: 27 Chain: "1" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2815 Classifications: {'peptide': 362} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 342} Chain: "3" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2789 Classifications: {'peptide': 358} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 338} Chain: "2" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2789 Classifications: {'peptide': 358} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 338} Chain: "D" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1167 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "B" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 798 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "A" Number of atoms: 5344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5344 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 26, 'TRANS': 640} Chain: "a" Number of atoms: 5309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5309 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 26, 'TRANS': 635} Chain: "4" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2815 Classifications: {'peptide': 362} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 342} Chain: "6" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2789 Classifications: {'peptide': 358} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 338} Chain: "5" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2789 Classifications: {'peptide': 358} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 338} Chain: "E" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 285 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'TRANS': 56} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'UNK:plan-1': 57} Unresolved non-hydrogen planarities: 57 Chain: "F" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 379 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "C" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 875 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "c" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 875 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "1" Number of atoms: 585 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 9, 585 Unusual residues: {'BCL': 8, 'CDL': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "3" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 462 Unusual residues: {'BCL': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "2" Number of atoms: 554 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 9, 554 Unusual residues: {'BCL': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1119 Unusual residues: {' CA': 1, 'BCL': 11, 'F39': 2, 'G2O': 2, 'GS0': 1, 'LHG': 3, 'LMG': 1, 'SF4': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'BCL:plan_0002': 6} Unresolved non-hydrogen planarities: 36 Chain: "a" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 1232 Unusual residues: {' CA': 1, 'BCL': 11, 'CDL': 2, 'F26': 1, 'F39': 1, 'G2O': 2, 'GS0': 1, 'LHG': 3, 'LMG': 1} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'BCL:plan_0002': 6} Unresolved non-hydrogen planarities: 36 Chain: "4" Number of atoms: 620 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 10, 620 Unusual residues: {'BCL': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "6" Number of atoms: 508 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 8, 508 Unusual residues: {'BCL': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "5" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 396 Unusual residues: {'BCL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'F39': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "c" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'BCL': 1, 'CDL': 1, 'F26': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9680 SG CYS B 143 66.823 84.125 104.768 1.00 43.20 S ATOM 9663 SG CYS B 140 68.050 90.131 106.788 1.00 43.27 S ATOM 10035 SG CYS B 191 66.686 88.686 100.449 1.00 45.00 S ATOM 9698 SG CYS B 146 72.206 86.871 103.894 1.00 43.16 S ATOM 9974 SG CYS B 182 82.343 86.204 97.127 1.00 49.79 S ATOM 9729 SG CYS B 150 80.027 86.081 102.421 1.00 45.60 S ATOM 9991 SG CYS B 185 75.697 88.128 98.260 1.00 44.17 S ATOM 9954 SG CYS B 179 80.615 91.782 98.885 1.00 46.38 S ATOM 19615 SG CYS a 536 65.628 74.332 113.703 1.00 41.90 S ATOM 14306 SG CYS A 536 59.191 76.729 112.707 1.00 39.43 S ATOM 14247 SG CYS A 527 64.046 77.537 108.827 1.00 42.57 S ATOM 19556 SG CYS a 527 64.223 79.558 115.026 1.00 41.72 S Time building chain proxies: 7.84, per 1000 atoms: 0.21 Number of scatterers: 37660 At special positions: 0 Unit cell: (108.56, 169.28, 185.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 12 26.01 Ca 2 19.99 S 139 16.00 P 15 15.00 Mg 79 11.99 O 6326 8.00 N 5745 7.00 C 25342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=96, symmetry=0 Number of additional bonds: simple=96, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 821 " pdb="FE3 SF4 A 821 " - pdb=" SG CYS A 527 " pdb="FE4 SF4 A 821 " - pdb=" SG CYS a 527 " pdb="FE2 SF4 A 821 " - pdb=" SG CYS A 536 " pdb="FE1 SF4 A 821 " - pdb=" SG CYS a 536 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 143 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 140 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 146 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 191 " pdb=" SF4 B 302 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 185 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 179 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 150 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 182 " Number of angles added : 36 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7360 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 16 sheets defined 40.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain '1' and resid 127 through 132 removed outlier: 3.615A pdb=" N ARG 1 131 " --> pdb=" O SER 1 127 " (cutoff:3.500A) Processing helix chain '1' and resid 156 through 173 Processing helix chain '1' and resid 175 through 185 removed outlier: 5.150A pdb=" N ARG 1 181 " --> pdb=" O ASN 1 177 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP 1 182 " --> pdb=" O ASP 1 178 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE 1 183 " --> pdb=" O TRP 1 179 " (cutoff:3.500A) Processing helix chain '1' and resid 187 through 195 removed outlier: 4.091A pdb=" N THR 1 191 " --> pdb=" O GLY 1 187 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN 1 194 " --> pdb=" O PHE 1 190 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU 1 195 " --> pdb=" O THR 1 191 " (cutoff:3.500A) Processing helix chain '1' and resid 233 through 238 Processing helix chain '1' and resid 291 through 299 removed outlier: 3.937A pdb=" N LEU 1 295 " --> pdb=" O PRO 1 291 " (cutoff:3.500A) Processing helix chain '1' and resid 342 through 354 removed outlier: 3.689A pdb=" N ARG 1 347 " --> pdb=" O GLY 1 343 " (cutoff:3.500A) Processing helix chain '3' and resid 127 through 134 removed outlier: 3.517A pdb=" N ASN 3 133 " --> pdb=" O ALA 3 129 " (cutoff:3.500A) Processing helix chain '3' and resid 156 through 173 Processing helix chain '3' and resid 175 through 185 removed outlier: 5.143A pdb=" N ARG 3 181 " --> pdb=" O ASN 3 177 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP 3 182 " --> pdb=" O ASP 3 178 " (cutoff:3.500A) Processing helix chain '3' and resid 188 through 196 removed outlier: 3.720A pdb=" N ASN 3 194 " --> pdb=" O PHE 3 190 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 238 Processing helix chain '3' and resid 291 through 299 removed outlier: 3.874A pdb=" N LEU 3 295 " --> pdb=" O PRO 3 291 " (cutoff:3.500A) Processing helix chain '3' and resid 342 through 354 Processing helix chain '2' and resid 127 through 134 Processing helix chain '2' and resid 156 through 173 Processing helix chain '2' and resid 175 through 185 removed outlier: 4.775A pdb=" N ARG 2 181 " --> pdb=" O ASN 2 177 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP 2 182 " --> pdb=" O ASP 2 178 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE 2 183 " --> pdb=" O TRP 2 179 " (cutoff:3.500A) Processing helix chain '2' and resid 187 through 196 removed outlier: 4.431A pdb=" N THR 2 191 " --> pdb=" O GLY 2 187 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN 2 194 " --> pdb=" O PHE 2 190 " (cutoff:3.500A) Processing helix chain '2' and resid 233 through 238 removed outlier: 3.655A pdb=" N ARG 2 238 " --> pdb=" O ASP 2 234 " (cutoff:3.500A) Processing helix chain '2' and resid 291 through 302 removed outlier: 4.007A pdb=" N LEU 2 295 " --> pdb=" O PRO 2 291 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET 2 300 " --> pdb=" O VAL 2 296 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL 2 301 " --> pdb=" O HIS 2 297 " (cutoff:3.500A) Processing helix chain '2' and resid 343 through 355 Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 20 through 24 removed outlier: 3.830A pdb=" N TRP D 23 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 72 Processing helix chain 'D' and resid 89 through 99 Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.544A pdb=" N LYS B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.620A pdb=" N GLU B 167 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 71 through 97 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 117 through 124 Processing helix chain 'A' and resid 132 through 166 removed outlier: 3.674A pdb=" N ALA A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.538A pdb=" N VAL A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 228 removed outlier: 4.697A pdb=" N GLY A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 239 through 263 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 276 through 301 Processing helix chain 'A' and resid 302 through 307 removed outlier: 6.355A pdb=" N SER A 305 " --> pdb=" O GLN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 363 through 401 removed outlier: 3.555A pdb=" N ASN A 401 " --> pdb=" O LYS A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 419 through 452 Processing helix chain 'A' and resid 453 through 456 Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 471 through 475 removed outlier: 3.692A pdb=" N MET A 474 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 475 " --> pdb=" O GLN A 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 471 through 475' Processing helix chain 'A' and resid 479 through 506 removed outlier: 3.845A pdb=" N ALA A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 539 through 563 removed outlier: 4.100A pdb=" N LYS A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 554 " --> pdb=" O TRP A 550 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 597 through 601 Processing helix chain 'A' and resid 603 through 608 removed outlier: 3.819A pdb=" N ILE A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 627 removed outlier: 3.801A pdb=" N SER A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 634 through 656 removed outlier: 3.643A pdb=" N PHE A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 687 Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'a' and resid 48 through 54 removed outlier: 3.593A pdb=" N GLN a 52 " --> pdb=" O ARG a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 60 through 64 removed outlier: 3.868A pdb=" N ILE a 64 " --> pdb=" O TRP a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 70 Processing helix chain 'a' and resid 71 through 97 Processing helix chain 'a' and resid 111 through 124 removed outlier: 4.107A pdb=" N ILE a 117 " --> pdb=" O PHE a 113 " (cutoff:3.500A) Proline residue: a 119 - end of helix Processing helix chain 'a' and resid 132 through 166 Processing helix chain 'a' and resid 188 through 193 Processing helix chain 'a' and resid 201 through 204 Processing helix chain 'a' and resid 205 through 228 Processing helix chain 'a' and resid 239 through 263 removed outlier: 3.576A pdb=" N THR a 243 " --> pdb=" O ILE a 239 " (cutoff:3.500A) Processing helix chain 'a' and resid 268 through 273 removed outlier: 4.073A pdb=" N ASN a 272 " --> pdb=" O ALA a 268 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP a 273 " --> pdb=" O ILE a 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 268 through 273' Processing helix chain 'a' and resid 276 through 302 removed outlier: 4.061A pdb=" N GLN a 302 " --> pdb=" O PHE a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 307 Processing helix chain 'a' and resid 310 through 316 Processing helix chain 'a' and resid 363 through 401 Processing helix chain 'a' and resid 409 through 414 Processing helix chain 'a' and resid 419 through 452 Processing helix chain 'a' and resid 453 through 456 Processing helix chain 'a' and resid 457 through 461 Processing helix chain 'a' and resid 471 through 475 Processing helix chain 'a' and resid 479 through 506 removed outlier: 3.951A pdb=" N ALA a 499 " --> pdb=" O PHE a 495 " (cutoff:3.500A) Processing helix chain 'a' and resid 510 through 516 Processing helix chain 'a' and resid 530 through 534 Processing helix chain 'a' and resid 539 through 563 removed outlier: 4.164A pdb=" N LYS a 553 " --> pdb=" O LEU a 549 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY a 554 " --> pdb=" O TRP a 550 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL a 558 " --> pdb=" O GLY a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 581 through 586 Processing helix chain 'a' and resid 597 through 601 Processing helix chain 'a' and resid 604 through 610 removed outlier: 3.654A pdb=" N SER a 610 " --> pdb=" O THR a 606 " (cutoff:3.500A) Processing helix chain 'a' and resid 610 through 627 removed outlier: 3.630A pdb=" N SER a 627 " --> pdb=" O VAL a 623 " (cutoff:3.500A) Processing helix chain 'a' and resid 627 through 632 Processing helix chain 'a' and resid 634 through 653 Processing helix chain 'a' and resid 669 through 687 Processing helix chain 'a' and resid 688 through 694 Processing helix chain '4' and resid 127 through 132 Processing helix chain '4' and resid 156 through 173 Processing helix chain '4' and resid 175 through 184 removed outlier: 5.138A pdb=" N ARG 4 181 " --> pdb=" O ASN 4 177 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP 4 182 " --> pdb=" O ASP 4 178 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE 4 183 " --> pdb=" O TRP 4 179 " (cutoff:3.500A) Processing helix chain '4' and resid 188 through 196 removed outlier: 3.697A pdb=" N ASN 4 194 " --> pdb=" O PHE 4 190 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 238 Processing helix chain '4' and resid 291 through 303 removed outlier: 4.082A pdb=" N LEU 4 295 " --> pdb=" O PRO 4 291 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET 4 300 " --> pdb=" O VAL 4 296 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL 4 301 " --> pdb=" O HIS 4 297 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS 4 303 " --> pdb=" O GLY 4 299 " (cutoff:3.500A) Processing helix chain '4' and resid 342 through 354 Processing helix chain '6' and resid 127 through 132 removed outlier: 3.612A pdb=" N ARG 6 131 " --> pdb=" O SER 6 127 " (cutoff:3.500A) Processing helix chain '6' and resid 156 through 173 removed outlier: 3.516A pdb=" N ILE 6 160 " --> pdb=" O ASN 6 156 " (cutoff:3.500A) Processing helix chain '6' and resid 175 through 184 removed outlier: 5.277A pdb=" N ARG 6 181 " --> pdb=" O ASN 6 177 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP 6 182 " --> pdb=" O ASP 6 178 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE 6 183 " --> pdb=" O TRP 6 179 " (cutoff:3.500A) Processing helix chain '6' and resid 187 through 196 removed outlier: 4.412A pdb=" N THR 6 191 " --> pdb=" O GLY 6 187 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN 6 194 " --> pdb=" O PHE 6 190 " (cutoff:3.500A) Processing helix chain '6' and resid 233 through 238 Processing helix chain '6' and resid 238 through 243 removed outlier: 4.362A pdb=" N PHE 6 243 " --> pdb=" O TRP 6 239 " (cutoff:3.500A) Processing helix chain '6' and resid 291 through 302 removed outlier: 3.857A pdb=" N LEU 6 295 " --> pdb=" O PRO 6 291 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET 6 300 " --> pdb=" O VAL 6 296 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL 6 301 " --> pdb=" O HIS 6 297 " (cutoff:3.500A) Processing helix chain '6' and resid 342 through 354 removed outlier: 3.563A pdb=" N ARG 6 347 " --> pdb=" O GLY 6 343 " (cutoff:3.500A) Processing helix chain '5' and resid 127 through 134 removed outlier: 3.754A pdb=" N ARG 5 131 " --> pdb=" O SER 5 127 " (cutoff:3.500A) Processing helix chain '5' and resid 156 through 173 Processing helix chain '5' and resid 175 through 185 removed outlier: 4.790A pdb=" N ARG 5 181 " --> pdb=" O ASN 5 177 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP 5 182 " --> pdb=" O ASP 5 178 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE 5 183 " --> pdb=" O TRP 5 179 " (cutoff:3.500A) Processing helix chain '5' and resid 188 through 196 Processing helix chain '5' and resid 233 through 238 Processing helix chain '5' and resid 291 through 298 removed outlier: 3.913A pdb=" N LEU 5 295 " --> pdb=" O PRO 5 291 " (cutoff:3.500A) Processing helix chain '5' and resid 298 through 303 removed outlier: 3.908A pdb=" N LYS 5 303 " --> pdb=" O GLY 5 299 " (cutoff:3.500A) Processing helix chain '5' and resid 342 through 354 Processing helix chain 'E' and resid 5 through 14 Processing helix chain 'E' and resid 16 through 22 Processing helix chain 'E' and resid 33 through 41 removed outlier: 4.169A pdb=" N UNK E 37 " --> pdb=" O UNK E 33 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N UNK E 38 " --> pdb=" O UNK E 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 12 Processing helix chain 'F' and resid 12 through 17 Processing helix chain 'F' and resid 23 through 34 Processing helix chain 'F' and resid 36 through 48 removed outlier: 3.551A pdb=" N VAL F 40 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.594A pdb=" N VAL C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 72 removed outlier: 3.787A pdb=" N SER C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.531A pdb=" N PHE C 78 " --> pdb=" O ASP C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 99 removed outlier: 3.789A pdb=" N ARG C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 7 through 31 removed outlier: 3.663A pdb=" N PHE c 29 " --> pdb=" O PHE c 25 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU c 30 " --> pdb=" O SER c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 71 removed outlier: 3.807A pdb=" N LEU c 46 " --> pdb=" O ILE c 42 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS c 68 " --> pdb=" O MET c 64 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER c 70 " --> pdb=" O LEU c 66 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER c 71 " --> pdb=" O GLY c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 79 removed outlier: 4.451A pdb=" N LEU c 79 " --> pdb=" O LYS c 76 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 99 removed outlier: 3.694A pdb=" N ARG c 97 " --> pdb=" O PHE c 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 12 through 20 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 28 through 36 current: chain '1' and resid 64 through 75 removed outlier: 5.619A pdb=" N THR 1 112 " --> pdb=" O PRO 1 153 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 141 through 153 current: chain '1' and resid 217 through 230 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 217 through 230 current: chain '1' and resid 265 through 273 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 265 through 273 current: chain '1' and resid 337 through 341 Processing sheet with id=AA2, first strand: chain '1' and resid 277 through 279 removed outlier: 5.243A pdb=" N ILE 1 362 " --> pdb=" O ILE 1 287 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLU 1 361 " --> pdb=" O ALA 1 326 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA 1 326 " --> pdb=" O GLU 1 361 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU 1 363 " --> pdb=" O ARG 1 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 11 through 20 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 28 through 36 current: chain '3' and resid 64 through 75 removed outlier: 5.620A pdb=" N THR 3 112 " --> pdb=" O PRO 3 153 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 142 through 153 current: chain '3' and resid 218 through 224 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 218 through 224 current: chain '3' and resid 264 through 273 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 264 through 273 current: chain '3' and resid 337 through 341 Processing sheet with id=AA4, first strand: chain '3' and resid 277 through 281 removed outlier: 5.683A pdb=" N LEU 3 284 " --> pdb=" O ALA 3 280 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU 3 363 " --> pdb=" O ARG 3 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 11 through 20 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 28 through 36 current: chain '2' and resid 64 through 75 removed outlier: 5.878A pdb=" N THR 2 112 " --> pdb=" O PRO 2 153 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '2' and resid 142 through 153 current: chain '2' and resid 217 through 229 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 217 through 229 current: chain '2' and resid 264 through 269 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 264 through 269 current: chain '2' and resid 337 through 341 Processing sheet with id=AA6, first strand: chain '2' and resid 277 through 279 removed outlier: 5.180A pdb=" N ILE 2 362 " --> pdb=" O ILE 2 287 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU 2 361 " --> pdb=" O ALA 2 326 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA 2 326 " --> pdb=" O GLU 2 361 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU 2 363 " --> pdb=" O ARG 2 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 51 through 53 removed outlier: 11.925A pdb=" N ILE D 75 " --> pdb=" O TYR D 121 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N TYR D 121 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE D 77 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU D 130 " --> pdb=" O PRO D 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 40 through 41 removed outlier: 3.625A pdb=" N LYS D 40 " --> pdb=" O GLN D 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AB1, first strand: chain 'A' and resid 317 through 318 removed outlier: 3.519A pdb=" N LYS A 357 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '4' and resid 12 through 20 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 28 through 36 current: chain '4' and resid 64 through 75 removed outlier: 5.547A pdb=" N THR 4 112 " --> pdb=" O PRO 4 153 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '4' and resid 142 through 153 current: chain '4' and resid 217 through 229 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 217 through 229 current: chain '4' and resid 265 through 269 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 265 through 269 current: chain '4' and resid 337 through 340 Processing sheet with id=AB3, first strand: chain '4' and resid 277 through 281 removed outlier: 5.707A pdb=" N LEU 4 284 " --> pdb=" O ALA 4 280 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILE 4 362 " --> pdb=" O ILE 4 287 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU 4 361 " --> pdb=" O ALA 4 326 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA 4 326 " --> pdb=" O GLU 4 361 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU 4 363 " --> pdb=" O ARG 4 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '6' and resid 11 through 20 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 28 through 36 current: chain '6' and resid 65 through 75 removed outlier: 5.789A pdb=" N THR 6 112 " --> pdb=" O PRO 6 153 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '6' and resid 142 through 153 current: chain '6' and resid 217 through 229 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 217 through 229 current: chain '6' and resid 264 through 273 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 264 through 273 current: chain '6' and resid 337 through 341 Processing sheet with id=AB5, first strand: chain '6' and resid 277 through 281 removed outlier: 6.150A pdb=" N LEU 6 284 " --> pdb=" O ALA 6 280 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE 6 362 " --> pdb=" O ILE 6 287 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLU 6 361 " --> pdb=" O ALA 6 326 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA 6 326 " --> pdb=" O GLU 6 361 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU 6 363 " --> pdb=" O ARG 6 324 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '5' and resid 11 through 20 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 28 through 36 current: chain '5' and resid 64 through 75 removed outlier: 5.489A pdb=" N THR 5 112 " --> pdb=" O PRO 5 153 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '5' and resid 142 through 153 current: chain '5' and resid 217 through 229 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 217 through 229 current: chain '5' and resid 264 through 269 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 264 through 269 current: chain '5' and resid 337 through 341 Processing sheet with id=AB7, first strand: chain '5' and resid 277 through 281 removed outlier: 6.355A pdb=" N LEU 5 284 " --> pdb=" O ALA 5 280 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE 5 362 " --> pdb=" O ILE 5 287 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLU 5 361 " --> pdb=" O ALA 5 326 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA 5 326 " --> pdb=" O GLU 5 361 " (cutoff:3.500A) 1388 hydrogen bonds defined for protein. 3972 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: 7.07 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.34: 11020 1.34 - 1.58: 27387 1.58 - 1.82: 421 1.82 - 2.06: 234 2.06 - 2.30: 118 Bond restraints: 39180 Sorted by residual: bond pdb=" C32 F39 A 815 " pdb=" C35 F39 A 815 " ideal model delta sigma weight residual 1.349 1.651 -0.302 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C32 F39 a 816 " pdb=" C35 F39 a 816 " ideal model delta sigma weight residual 1.349 1.650 -0.301 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C40 F39 C 302 " pdb=" C41 F39 C 302 " ideal model delta sigma weight residual 1.352 1.653 -0.301 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C40 F39 A 814 " pdb=" C41 F39 A 814 " ideal model delta sigma weight residual 1.352 1.652 -0.300 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C40 F39 A 815 " pdb=" C41 F39 A 815 " ideal model delta sigma weight residual 1.352 1.651 -0.299 2.00e-02 2.50e+03 2.24e+02 ... (remaining 39175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 50857 3.84 - 7.68: 2804 7.68 - 11.52: 478 11.52 - 15.36: 93 15.36 - 19.20: 21 Bond angle restraints: 54253 Sorted by residual: angle pdb=" C11 CDL a 820 " pdb=" CA5 CDL a 820 " pdb=" OA6 CDL a 820 " ideal model delta sigma weight residual 111.33 120.86 -9.53 1.32e+00 5.72e-01 5.20e+01 angle pdb=" C11 CDL 1 409 " pdb=" CA5 CDL 1 409 " pdb=" OA6 CDL 1 409 " ideal model delta sigma weight residual 111.33 120.34 -9.01 1.32e+00 5.72e-01 4.65e+01 angle pdb=" C51 CDL a 820 " pdb=" CB5 CDL a 820 " pdb=" OB6 CDL a 820 " ideal model delta sigma weight residual 111.33 120.34 -9.01 1.32e+00 5.72e-01 4.64e+01 angle pdb=" C51 CDL c 303 " pdb=" CB5 CDL c 303 " pdb=" OB6 CDL c 303 " ideal model delta sigma weight residual 111.33 120.25 -8.92 1.32e+00 5.72e-01 4.55e+01 angle pdb=" C51 CDL 1 409 " pdb=" CB5 CDL 1 409 " pdb=" OB6 CDL 1 409 " ideal model delta sigma weight residual 111.33 120.23 -8.90 1.32e+00 5.72e-01 4.53e+01 ... (remaining 54248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 20447 35.99 - 71.99: 771 71.99 - 107.98: 96 107.98 - 143.98: 27 143.98 - 179.97: 12 Dihedral angle restraints: 21353 sinusoidal: 9810 harmonic: 11543 Sorted by residual: dihedral pdb=" CBD BCL 6 401 " pdb=" CGD BCL 6 401 " pdb=" O2D BCL 6 401 " pdb=" CED BCL 6 401 " ideal model delta sinusoidal sigma weight residual 180.00 0.03 179.97 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CBD BCL 3 401 " pdb=" CGD BCL 3 401 " pdb=" O2D BCL 3 401 " pdb=" CED BCL 3 401 " ideal model delta sinusoidal sigma weight residual 180.00 0.07 179.93 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CBD BCL 2 403 " pdb=" CGD BCL 2 403 " pdb=" O2D BCL 2 403 " pdb=" CED BCL 2 403 " ideal model delta sinusoidal sigma weight residual 180.00 0.10 179.90 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 21350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.123: 5373 1.123 - 2.246: 0 2.246 - 3.368: 0 3.368 - 4.491: 0 4.491 - 5.614: 2 Chirality restraints: 5375 Sorted by residual: chirality pdb=" C18 BCL a 806 " pdb=" C17 BCL a 806 " pdb=" C19 BCL a 806 " pdb=" C20 BCL a 806 " both_signs ideal model delta sigma weight residual False 2.71 -2.90 5.61 2.00e-01 2.50e+01 7.88e+02 chirality pdb=" C18 BCL A 805 " pdb=" C17 BCL A 805 " pdb=" C19 BCL A 805 " pdb=" C20 BCL A 805 " both_signs ideal model delta sigma weight residual False 2.71 -2.89 5.60 2.00e-01 2.50e+01 7.85e+02 chirality pdb=" CBD G2O A 802 " pdb=" CAD G2O A 802 " pdb=" CGD G2O A 802 " pdb=" CHA G2O A 802 " both_signs ideal model delta sigma weight residual False 2.80 2.01 0.79 2.00e-01 2.50e+01 1.55e+01 ... (remaining 5372 not shown) Planarity restraints: 6672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 F39 a 816 " 0.119 2.00e-02 2.50e+03 5.05e-01 3.19e+03 pdb=" C20 F39 a 816 " -0.492 2.00e-02 2.50e+03 pdb=" C25 F39 a 816 " 0.490 2.00e-02 2.50e+03 pdb=" C27 F39 a 816 " -0.680 2.00e-02 2.50e+03 pdb=" C32 F39 a 816 " 0.563 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 F39 C 302 " 0.483 2.00e-02 2.50e+03 4.20e-01 2.20e+03 pdb=" C42 F39 C 302 " -0.488 2.00e-02 2.50e+03 pdb=" C43 F39 C 302 " 0.003 2.00e-02 2.50e+03 pdb=" C44 F39 C 302 " -0.453 2.00e-02 2.50e+03 pdb=" C51 F39 C 302 " 0.454 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 F39 A 815 " -0.445 2.00e-02 2.50e+03 3.76e-01 1.77e+03 pdb=" C42 F39 A 815 " 0.478 2.00e-02 2.50e+03 pdb=" C43 F39 A 815 " -0.004 2.00e-02 2.50e+03 pdb=" C44 F39 A 815 " 0.360 2.00e-02 2.50e+03 pdb=" C51 F39 A 815 " -0.389 2.00e-02 2.50e+03 ... (remaining 6669 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 5428 2.76 - 3.47: 53974 3.47 - 4.19: 104872 4.19 - 4.90: 183413 Nonbonded interactions: 347689 Sorted by model distance: nonbonded pdb=" CE1 HIS 3 146 " pdb="MG BCL 3 405 " model vdw 1.331 3.130 nonbonded pdb=" NE2 HIS 3 146 " pdb="MG BCL 3 405 " model vdw 1.899 2.990 nonbonded pdb=" OG1 THR a 509 " pdb=" OD1 ASP a 514 " model vdw 2.120 3.040 nonbonded pdb=" OH TYR B 133 " pdb=" OG SER B 183 " model vdw 2.128 3.040 nonbonded pdb=" OG SER D 20 " pdb=" OD2 ASP B 217 " model vdw 2.143 3.040 ... (remaining 347684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and (resid 9 through 401 or (resid 402 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )) or resid 403 through 406)) selection = (chain '2' and resid 9 through 406) selection = (chain '3' and (resid 9 through 401 or (resid 402 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )) or resid 403 through 406)) selection = (chain '4' and (resid 9 through 401 or (resid 402 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )) or resid 403 through 406)) selection = (chain '5' and (resid 9 through 401 or (resid 402 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )) or resid 403 through 406)) selection = (chain '6' and (resid 9 through 401 or (resid 402 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )) or resid 403 through 406)) } ncs_group { reference = (chain 'A' and (resid 47 through 708 or (resid 804 and (name NB or name ND or na \ me C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C o \ r name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C \ 4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or na \ me CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD o \ r name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name C \ MC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )) or (resid 805 and (name NB or name ND \ or name C1 or name C10 or name C1A or name C1B or name C1C or name C1D or name \ C2 or name C2A or name C2B or name C2C or name C2D or name C3 or name C3A or nam \ e C3B or name C3C or name C3D or name C4 or name C4A or name C4B or name C4C or \ name C4D or name C5 or name C6 or name C7 or name C8 or name C9 or name CAA or n \ ame CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD \ or name CED or name CGA or name CGD or name CHA or name CHB or name CHC or name \ CHD or name CMA or name CMB or name CMC or name CMD or name NA or name NC or nam \ e O1A or name O1D or name O2A or name O2D or name OBB or name OBD or name MG )) \ or (resid 806 through 810 and (name NB or name ND or name C1A or name C1B or nam \ e C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3A or \ name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name C4 \ D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or nam \ e CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CHB or \ name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA \ or name NC or name O1A or name O1D or name O2A or name O2D or name OBB or name \ OBD or name MG )) or resid 811 through 813 or (resid 819 and (name C1 or name C1 \ 0 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or nam \ e C17 or name C18 or name C2 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or \ name O1 or name O10 or name O2 or name O3 or name O4 or name O5 or name O6 or n \ ame O7 or name O8 or name O9 or name P )))) selection = (chain 'a' and (resid 47 through 708 or resid 804 through 805 or (resid 806 thro \ ugh 810 and (name NB or name ND or name C1A or name C1B or name C1C or name C1D \ or name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name \ C3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or n \ ame CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD \ or name CED or name CGA or name CGD or name CHA or name CHB or name CHC or name \ CHD or name CMA or name CMB or name CMC or name CMD or name NA or name NC or nam \ e O1A or name O1D or name O2A or name O2D or name OBB or name OBD or name MG )) \ or resid 811 or (resid 812 through 813 and (name NB or name ND or name C1A or na \ me C1B or name C1C or name C1D or name C2A or name C2B or name C2C or name C2D o \ r name C3A or name C3B or name C3C or name C3D or name C4A or name C4B or name C \ 4C or name C4D or name CAA or name CAB or name CAC or name CAD or name CBA or na \ me CBB or name CBC or name CBD or name CED or name CGA or name CGD or name CHA o \ r name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or name C \ MD or name NA or name NC or name O1A or name O1D or name O2A or name O2D or name \ OBB or name OBD or name MG )) or resid 819)) } ncs_group { reference = (chain 'C' and resid 6 through 301) selection = (chain 'c' and resid 6 through 301) } 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 38.130 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 : 0.026 0.577 39288 Z= 1.717 Angle : 1.892 23.290 54289 Z= 0.781 Chirality : 0.165 5.614 5375 Planarity : 0.030 0.505 6672 Dihedral : 19.220 179.969 13993 Min Nonbonded Distance : 1.331 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.68 % Favored : 94.15 % Rotamer: Outliers : 0.06 % Allowed : 0.24 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 3980 helix: -0.03 (0.14), residues: 1405 sheet: 0.11 (0.18), residues: 919 loop : -1.66 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 176 TYR 0.031 0.002 TYR 5 321 PHE 0.038 0.002 PHE A 692 TRP 0.059 0.002 TRP 3 184 HIS 0.010 0.001 HIS 3 351 Details of bonding type rmsd/Z covalent geometry : bond 0.02117 / 0.97 (39180) covalent geometry : angle 1.87779 / 0.78 (54253) hydrogen bonds : bond 0.17777 / 11.83 ( 1388) hydrogen bonds : angle 7.62570 / 5.47 ( 3972) metal coordination : bond 0.01309 / 0.93 ( 12) metal coordination : angle 9.14970 / 6.70 ( 36) Misc. bond : bond 0.30255 / 22.04 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 576 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 103 MET cc_start: 0.7375 (ppp) cc_final: 0.7051 (ttm) REVERT: 2 201 SER cc_start: 0.8776 (p) cc_final: 0.8542 (p) REVERT: A 302 GLN cc_start: 0.7725 (mt0) cc_final: 0.7476 (mp10) REVERT: A 532 TYR cc_start: 0.8676 (m-80) cc_final: 0.7865 (m-80) REVERT: a 110 ASP cc_start: 0.7406 (m-30) cc_final: 0.7162 (m-30) REVERT: 6 325 TYR cc_start: 0.7677 (t80) cc_final: 0.7477 (t80) outliers start: 2 outliers final: 5 residues processed: 576 average time/residue: 0.6668 time to fit residues: 471.7968 Evaluate side-chains 420 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 415 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 170 ILE Chi-restraints excluded: chain 2 residue 253 GLN Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain 4 residue 50 ASP Chi-restraints excluded: chain 6 residue 209 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 206 ASN 1 305 ASN 3 133 ASN 3 136 ASN 3 359 GLN D 99 ASN A 418 GLN a 52 GLN a 99 GLN a 237 GLN ** 4 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 312 GLN ** 5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 329 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.139999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125266 restraints weight = 50928.787| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.58 r_work: 0.3386 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.589 39288 Z= 0.192 Angle : 0.909 27.244 54289 Z= 0.367 Chirality : 0.046 0.389 5375 Planarity : 0.005 0.070 6672 Dihedral : 16.792 179.621 6824 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.58 % Favored : 94.25 % Rotamer: Outliers : 1.56 % Allowed : 10.25 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 3980 helix: 0.10 (0.13), residues: 1442 sheet: 0.00 (0.18), residues: 911 loop : -1.71 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 2 339 TYR 0.022 0.002 TYR 5 321 PHE 0.044 0.002 PHE B 226 TRP 0.018 0.001 TRP C 52 HIS 0.009 0.002 HIS 1 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (39180) covalent geometry : angle 0.87228 / 0.37 (54253) hydrogen bonds : bond 0.04377 / 2.98 ( 1388) hydrogen bonds : angle 5.71371 / 4.08 ( 3972) metal coordination : bond 0.01256 / 0.87 ( 12) metal coordination : angle 10.00157 / 7.41 ( 36) Misc. bond : bond 0.09645 / 7.60 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 474 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 21 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: 1 308 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.7203 (p0) REVERT: 3 103 MET cc_start: 0.8139 (ppp) cc_final: 0.7402 (ttm) REVERT: 3 312 GLN cc_start: 0.7673 (tt0) cc_final: 0.7296 (tt0) REVERT: 2 79 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8175 (mtmt) REVERT: 2 201 SER cc_start: 0.8960 (p) cc_final: 0.8746 (p) REVERT: A 302 GLN cc_start: 0.8128 (mt0) cc_final: 0.7661 (mp10) REVERT: A 532 TYR cc_start: 0.8867 (m-80) cc_final: 0.8071 (m-80) REVERT: A 701 ASN cc_start: 0.8397 (t0) cc_final: 0.8170 (t0) REVERT: a 110 ASP cc_start: 0.7989 (m-30) cc_final: 0.7656 (m-30) REVERT: a 163 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7680 (mmm-85) REVERT: 4 17 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7496 (pt0) REVERT: 4 322 LYS cc_start: 0.7402 (tttt) cc_final: 0.6754 (pmtt) REVERT: 6 103 MET cc_start: 0.8266 (pp-130) cc_final: 0.7895 (pp-130) REVERT: 6 150 MET cc_start: 0.8647 (ptt) cc_final: 0.8415 (ptt) REVERT: 6 266 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: 5 52 LYS cc_start: 0.8074 (tttt) cc_final: 0.7849 (tttt) REVERT: 5 224 ARG cc_start: 0.8490 (ptp90) cc_final: 0.8286 (ptp90) REVERT: 5 266 GLU cc_start: 0.7919 (tt0) cc_final: 0.7586 (mp0) REVERT: C 102 LYS cc_start: 0.7741 (mttp) cc_final: 0.7445 (mttm) outliers start: 52 outliers final: 19 residues processed: 502 average time/residue: 0.6582 time to fit residues: 407.8563 Evaluate side-chains 431 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 407 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 21 GLU Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 308 ASN Chi-restraints excluded: chain 3 residue 170 ILE Chi-restraints excluded: chain 2 residue 79 LYS Chi-restraints excluded: chain 2 residue 235 SER Chi-restraints excluded: chain 2 residue 253 GLN Chi-restraints excluded: chain 2 residue 331 ARG Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain a residue 73 GLU Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 64 PHE Chi-restraints excluded: chain 6 residue 14 SER Chi-restraints excluded: chain 6 residue 79 LYS Chi-restraints excluded: chain 6 residue 209 ASN Chi-restraints excluded: chain 6 residue 266 GLU Chi-restraints excluded: chain 5 residue 9 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain c residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 33 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 271 optimal weight: 10.0000 chunk 260 optimal weight: 0.4980 chunk 384 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 194 ASN 3 198 GLN 3 359 GLN 2 253 GLN ** 2 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 52 GLN a 179 ASN a 237 GLN a 645 GLN a 662 ASN ** 6 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 305 ASN 6 312 GLN 5 177 ASN 5 253 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122698 restraints weight = 51113.141| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.57 r_work: 0.3350 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.480 39288 Z= 0.183 Angle : 0.830 28.076 54289 Z= 0.337 Chirality : 0.044 0.200 5375 Planarity : 0.004 0.059 6672 Dihedral : 15.164 179.892 6820 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.80 % Favored : 94.05 % Rotamer: Outliers : 2.46 % Allowed : 13.68 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.28 % 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: -0.95 (0.13), residues: 3980 helix: 0.21 (0.13), residues: 1436 sheet: -0.09 (0.18), residues: 911 loop : -1.66 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 2 339 TYR 0.026 0.002 TYR 5 321 PHE 0.046 0.002 PHE B 226 TRP 0.023 0.001 TRP 4 184 HIS 0.008 0.002 HIS 2 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (39180) covalent geometry : angle 0.78743 / 0.34 (54253) hydrogen bonds : bond 0.04101 / 2.79 ( 1388) hydrogen bonds : angle 5.36612 / 3.84 ( 3972) metal coordination : bond 0.01508 / 1.02 ( 12) metal coordination : angle 10.21775 / 7.59 ( 36) Misc. bond : bond 0.08087 / 6.25 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 468 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 21 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: 1 101 GLU cc_start: 0.8072 (pp20) cc_final: 0.7727 (pp20) REVERT: 1 308 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.7203 (p0) REVERT: 3 103 MET cc_start: 0.8080 (ppp) cc_final: 0.7432 (ttm) REVERT: 3 232 MET cc_start: 0.8568 (mtp) cc_final: 0.8302 (mtp) REVERT: 3 312 GLN cc_start: 0.7610 (tt0) cc_final: 0.7245 (tt0) REVERT: 2 17 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: 2 79 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8201 (mtmt) REVERT: D 121 TYR cc_start: 0.7938 (t80) cc_final: 0.7598 (t80) REVERT: A 532 TYR cc_start: 0.8848 (m-80) cc_final: 0.8050 (m-80) REVERT: A 701 ASN cc_start: 0.8375 (t0) cc_final: 0.8114 (t0) REVERT: a 73 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7425 (tp30) REVERT: a 110 ASP cc_start: 0.8013 (m-30) cc_final: 0.7689 (m-30) REVERT: a 270 HIS cc_start: 0.7465 (m90) cc_final: 0.7256 (m90) REVERT: 4 93 LYS cc_start: 0.7864 (tmtt) cc_final: 0.7653 (tmtt) REVERT: 4 204 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: 4 322 LYS cc_start: 0.7386 (tttt) cc_final: 0.6827 (pmtt) REVERT: 6 131 ARG cc_start: 0.8001 (ttp-110) cc_final: 0.7628 (ttp80) REVERT: 6 266 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: c 92 MET cc_start: 0.5509 (mtt) cc_final: 0.4895 (mtp) outliers start: 82 outliers final: 35 residues processed: 514 average time/residue: 0.6535 time to fit residues: 417.9373 Evaluate side-chains 444 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 402 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 GLU Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 308 ASN Chi-restraints excluded: chain 3 residue 11 THR Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 64 PHE Chi-restraints excluded: chain 2 residue 79 LYS Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 2 residue 260 SER Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain a residue 73 GLU Chi-restraints excluded: chain a residue 132 LYS Chi-restraints excluded: chain a residue 470 ILE Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 64 PHE Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 4 residue 260 SER Chi-restraints excluded: chain 4 residue 278 VAL Chi-restraints excluded: chain 6 residue 14 SER Chi-restraints excluded: chain 6 residue 49 CYS Chi-restraints excluded: chain 6 residue 79 LYS Chi-restraints excluded: chain 6 residue 120 VAL Chi-restraints excluded: chain 6 residue 209 ASN Chi-restraints excluded: chain 6 residue 266 GLU Chi-restraints excluded: chain 6 residue 308 ASN Chi-restraints excluded: chain 6 residue 309 VAL Chi-restraints excluded: chain 5 residue 9 VAL Chi-restraints excluded: chain 5 residue 11 THR Chi-restraints excluded: chain 5 residue 48 ASP Chi-restraints excluded: chain 5 residue 103 MET Chi-restraints excluded: chain 5 residue 272 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain c residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 333 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 144 optimal weight: 0.0060 chunk 155 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 300 optimal weight: 9.9990 chunk 30 optimal weight: 0.3980 chunk 205 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 305 ASN 3 359 GLN 2 253 GLN D 99 ASN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 52 GLN ** a 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 237 GLN a 662 ASN ** 6 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 305 ASN 6 312 GLN ** 6 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125690 restraints weight = 50430.286| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.58 r_work: 0.3391 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.490 39288 Z= 0.144 Angle : 0.777 27.304 54289 Z= 0.318 Chirality : 0.043 0.218 5375 Planarity : 0.004 0.053 6672 Dihedral : 14.502 179.883 6815 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.28 % Favored : 94.57 % Rotamer: Outliers : 2.86 % Allowed : 15.72 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.13), residues: 3980 helix: 0.38 (0.14), residues: 1440 sheet: -0.07 (0.17), residues: 923 loop : -1.69 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 5 285 TYR 0.024 0.001 TYR a 114 PHE 0.028 0.001 PHE B 226 TRP 0.017 0.001 TRP 4 184 HIS 0.007 0.001 HIS 2 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (39180) covalent geometry : angle 0.73281 / 0.32 (54253) hydrogen bonds : bond 0.03747 / 2.56 ( 1388) hydrogen bonds : angle 5.17465 / 3.71 ( 3972) metal coordination : bond 0.01088 / 0.76 ( 12) metal coordination : angle 10.03179 / 7.47 ( 36) Misc. bond : bond 0.07940 / 6.23 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 448 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 156 ASN cc_start: 0.7742 (m110) cc_final: 0.7533 (m110) REVERT: 1 272 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: 1 308 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.7137 (p0) REVERT: 1 331 ARG cc_start: 0.7753 (tmm160) cc_final: 0.7453 (tmm160) REVERT: 3 103 MET cc_start: 0.8077 (ppp) cc_final: 0.7472 (ttm) REVERT: 3 232 MET cc_start: 0.8584 (mtp) cc_final: 0.8348 (mtp) REVERT: 3 312 GLN cc_start: 0.7501 (tt0) cc_final: 0.7162 (tt0) REVERT: 2 72 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7514 (tm-30) REVERT: 2 200 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8295 (mm) REVERT: 2 312 GLN cc_start: 0.8564 (tt0) cc_final: 0.8277 (tp40) REVERT: 2 325 TYR cc_start: 0.8348 (t80) cc_final: 0.8105 (t80) REVERT: D 47 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6556 (pt) REVERT: A 352 TYR cc_start: 0.8172 (m-80) cc_final: 0.7725 (m-80) REVERT: A 532 TYR cc_start: 0.8865 (m-80) cc_final: 0.7976 (m-80) REVERT: A 701 ASN cc_start: 0.8310 (t0) cc_final: 0.8018 (t0) REVERT: a 73 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: a 110 ASP cc_start: 0.7982 (m-30) cc_final: 0.7677 (m-30) REVERT: a 163 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7475 (mmm-85) REVERT: a 222 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8673 (mp) REVERT: a 237 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8125 (mp-120) REVERT: a 270 HIS cc_start: 0.7373 (m90) cc_final: 0.7112 (m90) REVERT: a 408 LYS cc_start: 0.8226 (mptt) cc_final: 0.8026 (mmtm) REVERT: 4 322 LYS cc_start: 0.7344 (tttt) cc_final: 0.6780 (pmtt) REVERT: 6 266 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6875 (tm-30) REVERT: 5 17 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7100 (mp0) REVERT: 5 266 GLU cc_start: 0.7863 (tt0) cc_final: 0.7651 (mp0) REVERT: 5 300 MET cc_start: 0.5734 (ptt) cc_final: 0.5377 (ptt) REVERT: c 92 MET cc_start: 0.5492 (mtt) cc_final: 0.5185 (mmm) outliers start: 95 outliers final: 37 residues processed: 508 average time/residue: 0.6169 time to fit residues: 392.0709 Evaluate side-chains 455 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 409 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 272 GLU Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 308 ASN Chi-restraints excluded: chain 3 residue 309 VAL Chi-restraints excluded: chain 2 residue 64 PHE Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 2 residue 200 ILE Chi-restraints excluded: chain 2 residue 253 GLN Chi-restraints excluded: chain 2 residue 260 SER Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 302 GLN Chi-restraints excluded: chain a residue 73 GLU Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 211 VAL Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain a residue 237 GLN Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 470 ILE Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 260 SER Chi-restraints excluded: chain 4 residue 278 VAL Chi-restraints excluded: chain 6 residue 14 SER Chi-restraints excluded: chain 6 residue 49 CYS Chi-restraints excluded: chain 6 residue 79 LYS Chi-restraints excluded: chain 6 residue 209 ASN Chi-restraints excluded: chain 6 residue 210 THR Chi-restraints excluded: chain 6 residue 266 GLU Chi-restraints excluded: chain 6 residue 301 VAL Chi-restraints excluded: chain 6 residue 308 ASN Chi-restraints excluded: chain 6 residue 309 VAL Chi-restraints excluded: chain 5 residue 9 VAL Chi-restraints excluded: chain 5 residue 48 ASP Chi-restraints excluded: chain 5 residue 103 MET Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 227 HIS Chi-restraints excluded: chain 5 residue 272 GLU Chi-restraints excluded: chain 5 residue 301 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain c residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 292 optimal weight: 5.9990 chunk 376 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 357 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 305 ASN 3 198 GLN 3 359 GLN 2 206 ASN ** 2 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN a 52 GLN ** a 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 521 ASN ** a 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 121 ASN ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 312 GLN ** 6 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115654 restraints weight = 51696.714| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.56 r_work: 0.3256 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.425 39288 Z= 0.335 Angle : 0.940 31.315 54289 Z= 0.386 Chirality : 0.049 0.329 5375 Planarity : 0.005 0.053 6672 Dihedral : 14.810 179.833 6815 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.67 % Rotamer: Outliers : 4.03 % Allowed : 16.56 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 3980 helix: 0.11 (0.13), residues: 1403 sheet: -0.36 (0.17), residues: 965 loop : -1.63 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 215 TYR 0.034 0.002 TYR 5 321 PHE 0.029 0.002 PHE B 226 TRP 0.028 0.002 TRP 4 184 HIS 0.011 0.002 HIS 1 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00823 / 0.33 (39180) covalent geometry : angle 0.90494 / 0.39 (54253) hydrogen bonds : bond 0.04401 / 2.99 ( 1388) hydrogen bonds : angle 5.45244 / 3.90 ( 3972) metal coordination : bond 0.02308 / 1.52 ( 12) metal coordination : angle 9.85369 / 7.25 ( 36) Misc. bond : bond 0.08766 / 6.47 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 424 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 21 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: 1 272 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: 1 308 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7418 (p0) REVERT: 3 103 MET cc_start: 0.8194 (ppp) cc_final: 0.7463 (ttm) REVERT: 3 268 LYS cc_start: 0.7421 (mttm) cc_final: 0.7213 (mtmm) REVERT: 3 312 GLN cc_start: 0.7873 (tt0) cc_final: 0.7456 (tt0) REVERT: 2 72 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: 2 200 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8526 (mm) REVERT: 2 238 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8254 (ptm160) REVERT: 2 312 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: 2 329 GLN cc_start: 0.8390 (tt0) cc_final: 0.8111 (pt0) REVERT: D 66 MET cc_start: 0.7881 (mmm) cc_final: 0.7624 (mmm) REVERT: A 271 LEU cc_start: 0.7959 (mm) cc_final: 0.7742 (mm) REVERT: A 325 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7584 (p90) REVERT: A 352 TYR cc_start: 0.8577 (m-80) cc_final: 0.7784 (m-80) REVERT: A 532 TYR cc_start: 0.8946 (m-80) cc_final: 0.8122 (m-80) REVERT: A 701 ASN cc_start: 0.8455 (t0) cc_final: 0.8204 (t0) REVERT: a 110 ASP cc_start: 0.8058 (m-30) cc_final: 0.7753 (m-30) REVERT: a 163 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7480 (mmm-85) REVERT: a 585 ILE cc_start: 0.8796 (tt) cc_final: 0.8547 (tt) REVERT: 4 85 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: 4 322 LYS cc_start: 0.7537 (tttt) cc_final: 0.6996 (pmtt) REVERT: 4 325 TYR cc_start: 0.7829 (t80) cc_final: 0.7615 (t80) REVERT: 6 204 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6678 (pm20) REVERT: 6 305 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.7088 (m110) REVERT: 5 323 ILE cc_start: 0.8835 (tt) cc_final: 0.8576 (tt) REVERT: F 8 LEU cc_start: 0.7017 (mt) cc_final: 0.6641 (tt) REVERT: F 18 MET cc_start: 0.7932 (mmt) cc_final: 0.7680 (mmt) REVERT: c 92 MET cc_start: 0.5578 (mtt) cc_final: 0.4985 (mmm) REVERT: c 96 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6273 (mm) outliers start: 134 outliers final: 62 residues processed: 513 average time/residue: 0.6450 time to fit residues: 411.9869 Evaluate side-chains 473 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 398 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 21 GLU Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 232 MET Chi-restraints excluded: chain 1 residue 272 GLU Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 301 VAL Chi-restraints excluded: chain 1 residue 308 ASN Chi-restraints excluded: chain 3 residue 11 THR Chi-restraints excluded: chain 3 residue 112 THR Chi-restraints excluded: chain 3 residue 170 ILE Chi-restraints excluded: chain 3 residue 309 VAL Chi-restraints excluded: chain 3 residue 324 ARG Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 72 GLU Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 200 ILE Chi-restraints excluded: chain 2 residue 218 VAL Chi-restraints excluded: chain 2 residue 238 ARG Chi-restraints excluded: chain 2 residue 260 SER Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 312 GLN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain a residue 73 GLU Chi-restraints excluded: chain a residue 132 LYS Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 211 VAL Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 460 MET Chi-restraints excluded: chain a residue 470 ILE Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 563 ASP Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 85 GLU Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 4 residue 278 VAL Chi-restraints excluded: chain 6 residue 49 CYS Chi-restraints excluded: chain 6 residue 79 LYS Chi-restraints excluded: chain 6 residue 120 VAL Chi-restraints excluded: chain 6 residue 204 GLU Chi-restraints excluded: chain 6 residue 209 ASN Chi-restraints excluded: chain 6 residue 301 VAL Chi-restraints excluded: chain 6 residue 305 ASN Chi-restraints excluded: chain 6 residue 308 ASN Chi-restraints excluded: chain 6 residue 309 VAL Chi-restraints excluded: chain 5 residue 9 VAL Chi-restraints excluded: chain 5 residue 48 ASP Chi-restraints excluded: chain 5 residue 103 MET Chi-restraints excluded: chain 5 residue 227 HIS Chi-restraints excluded: chain 5 residue 255 GLU Chi-restraints excluded: chain 5 residue 269 VAL Chi-restraints excluded: chain 5 residue 272 GLU Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 301 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 69 MET Chi-restraints excluded: chain c residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 48 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 79 optimal weight: 0.0040 chunk 361 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 295 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 137 optimal weight: 0.4980 chunk 201 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 305 ASN 3 194 ASN 3 359 GLN D 99 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN a 52 GLN ** a 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 121 ASN ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 305 ASN 6 312 GLN 6 329 GLN ** 6 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 263 GLN F 19 ASN ** c 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123732 restraints weight = 50607.606| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.56 r_work: 0.3367 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.480 39288 Z= 0.144 Angle : 0.773 27.896 54289 Z= 0.323 Chirality : 0.043 0.193 5375 Planarity : 0.004 0.052 6672 Dihedral : 14.294 179.976 6815 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.95 % Favored : 94.90 % Rotamer: Outliers : 2.58 % Allowed : 18.79 % Favored : 78.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.28 % 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: -0.89 (0.13), residues: 3980 helix: 0.39 (0.14), residues: 1403 sheet: -0.18 (0.17), residues: 931 loop : -1.67 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 4 339 TYR 0.023 0.002 TYR a 114 PHE 0.049 0.001 PHE B 226 TRP 0.016 0.001 TRP C 52 HIS 0.008 0.001 HIS 2 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (39180) covalent geometry : angle 0.73630 / 0.32 (54253) hydrogen bonds : bond 0.03748 / 2.55 ( 1388) hydrogen bonds : angle 5.15654 / 3.70 ( 3972) metal coordination : bond 0.01558 / 1.02 ( 12) metal coordination : angle 9.17111 / 6.76 ( 36) Misc. bond : bond 0.07900 / 6.19 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 452 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 156 ASN cc_start: 0.7901 (m110) cc_final: 0.7672 (m110) REVERT: 1 331 ARG cc_start: 0.7807 (tmm160) cc_final: 0.7588 (tmm160) REVERT: 3 54 ASN cc_start: 0.7548 (m-40) cc_final: 0.7341 (m-40) REVERT: 3 103 MET cc_start: 0.8123 (ppp) cc_final: 0.7442 (ttm) REVERT: 3 232 MET cc_start: 0.8420 (mtp) cc_final: 0.8198 (mtm) REVERT: 3 312 GLN cc_start: 0.7738 (tt0) cc_final: 0.7335 (tt0) REVERT: 2 200 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8387 (mm) REVERT: 2 312 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8269 (tp40) REVERT: 2 329 GLN cc_start: 0.8272 (tt0) cc_final: 0.8052 (pt0) REVERT: 2 330 TYR cc_start: 0.8589 (p90) cc_final: 0.8287 (p90) REVERT: A 419 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7941 (mt-10) REVERT: A 532 TYR cc_start: 0.8867 (m-80) cc_final: 0.7957 (m-80) REVERT: A 701 ASN cc_start: 0.8321 (t0) cc_final: 0.8065 (t0) REVERT: a 73 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7266 (tp30) REVERT: a 110 ASP cc_start: 0.8013 (m-30) cc_final: 0.7706 (m-30) REVERT: a 163 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7450 (mmm-85) REVERT: a 222 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8661 (mp) REVERT: 4 322 LYS cc_start: 0.7420 (tttt) cc_final: 0.6859 (pmtt) REVERT: 4 339 ARG cc_start: 0.7693 (ttm-80) cc_final: 0.7429 (ttm-80) REVERT: 6 204 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6716 (pm20) REVERT: 5 263 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: 5 300 MET cc_start: 0.6003 (ptt) cc_final: 0.5506 (ptt) REVERT: F 18 MET cc_start: 0.7746 (mmt) cc_final: 0.7512 (mmt) REVERT: c 92 MET cc_start: 0.5469 (mtt) cc_final: 0.5261 (mmm) outliers start: 86 outliers final: 41 residues processed: 510 average time/residue: 0.6408 time to fit residues: 407.8474 Evaluate side-chains 458 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 410 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 3 residue 309 VAL Chi-restraints excluded: chain 2 residue 64 PHE Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 200 ILE Chi-restraints excluded: chain 2 residue 260 SER Chi-restraints excluded: chain 2 residue 312 GLN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 302 GLN Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain a residue 73 GLU Chi-restraints excluded: chain a residue 132 LYS Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 211 VAL Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 470 ILE Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 260 SER Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 278 VAL Chi-restraints excluded: chain 6 residue 14 SER Chi-restraints excluded: chain 6 residue 49 CYS Chi-restraints excluded: chain 6 residue 79 LYS Chi-restraints excluded: chain 6 residue 120 VAL Chi-restraints excluded: chain 6 residue 204 GLU Chi-restraints excluded: chain 6 residue 209 ASN Chi-restraints excluded: chain 6 residue 301 VAL Chi-restraints excluded: chain 6 residue 309 VAL Chi-restraints excluded: chain 5 residue 9 VAL Chi-restraints excluded: chain 5 residue 48 ASP Chi-restraints excluded: chain 5 residue 103 MET Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 227 HIS Chi-restraints excluded: chain 5 residue 255 GLU Chi-restraints excluded: chain 5 residue 263 GLN Chi-restraints excluded: chain 5 residue 272 GLU Chi-restraints excluded: chain 5 residue 301 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain c residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 115 optimal weight: 6.9990 chunk 355 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 361 optimal weight: 0.2980 chunk 92 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 370 optimal weight: 10.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 305 ASN 2 206 ASN ** 2 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN A 171 ASN A 302 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN a 52 GLN 4 306 ASN ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 305 ASN 6 312 GLN ** 6 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.131044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116273 restraints weight = 51564.149| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.56 r_work: 0.3279 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.431 39288 Z= 0.279 Angle : 0.880 30.479 54289 Z= 0.362 Chirality : 0.047 0.203 5375 Planarity : 0.005 0.049 6672 Dihedral : 14.448 179.881 6815 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.01 % Favored : 93.84 % Rotamer: Outliers : 3.73 % Allowed : 18.85 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.13), residues: 3980 helix: 0.21 (0.13), residues: 1413 sheet: -0.37 (0.17), residues: 991 loop : -1.70 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 163 TYR 0.034 0.002 TYR A 599 PHE 0.041 0.002 PHE B 226 TRP 0.022 0.002 TRP 4 184 HIS 0.010 0.002 HIS 1 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.28 (39180) covalent geometry : angle 0.84315 / 0.36 (54253) hydrogen bonds : bond 0.04161 / 2.82 ( 1388) hydrogen bonds : angle 5.31385 / 3.80 ( 3972) metal coordination : bond 0.02691 / 1.77 ( 12) metal coordination : angle 9.83480 / 7.22 ( 36) Misc. bond : bond 0.08551 / 6.38 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 425 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 103 MET cc_start: 0.8195 (ppp) cc_final: 0.7451 (ttm) REVERT: 3 312 GLN cc_start: 0.7850 (tt0) cc_final: 0.7448 (tt0) REVERT: 2 198 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8568 (mt0) REVERT: 2 200 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8462 (mm) REVERT: 2 238 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8204 (ptm160) REVERT: 2 329 GLN cc_start: 0.8369 (tt0) cc_final: 0.8073 (pt0) REVERT: D 121 TYR cc_start: 0.7948 (t80) cc_final: 0.7672 (t80) REVERT: A 132 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.5805 (ptpp) REVERT: A 325 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7524 (p90) REVERT: A 352 TYR cc_start: 0.8538 (m-80) cc_final: 0.7959 (m-80) REVERT: A 532 TYR cc_start: 0.8925 (m-80) cc_final: 0.8077 (m-80) REVERT: A 701 ASN cc_start: 0.8439 (t0) cc_final: 0.8172 (t0) REVERT: a 73 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: a 110 ASP cc_start: 0.8058 (m-30) cc_final: 0.7747 (m-30) REVERT: a 163 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7443 (mmm-85) REVERT: 4 85 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: 4 204 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7800 (pt0) REVERT: 4 322 LYS cc_start: 0.7533 (tttt) cc_final: 0.6982 (pmtt) REVERT: 4 339 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7504 (ttm-80) REVERT: 6 204 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6722 (pm20) REVERT: 5 21 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: 5 199 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7685 (mtm-85) REVERT: 5 263 GLN cc_start: 0.8370 (pm20) cc_final: 0.8121 (pm20) REVERT: 5 323 ILE cc_start: 0.8798 (tt) cc_final: 0.8548 (tt) REVERT: F 8 LEU cc_start: 0.7008 (mt) cc_final: 0.6664 (tt) REVERT: F 18 MET cc_start: 0.7911 (mmt) cc_final: 0.7651 (mmt) outliers start: 124 outliers final: 64 residues processed: 502 average time/residue: 0.6243 time to fit residues: 389.8581 Evaluate side-chains 473 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 397 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 103 MET Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 186 ILE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 301 VAL Chi-restraints excluded: chain 3 residue 11 THR Chi-restraints excluded: chain 3 residue 170 ILE Chi-restraints excluded: chain 3 residue 309 VAL Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 198 GLN Chi-restraints excluded: chain 2 residue 200 ILE Chi-restraints excluded: chain 2 residue 218 VAL Chi-restraints excluded: chain 2 residue 238 ARG Chi-restraints excluded: chain 2 residue 260 SER Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain a residue 73 GLU Chi-restraints excluded: chain a residue 132 LYS Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 211 VAL Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 470 ILE Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 563 ASP Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 85 GLU Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 128 ASP Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 4 residue 260 SER Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 278 VAL Chi-restraints excluded: chain 4 residue 306 ASN Chi-restraints excluded: chain 6 residue 49 CYS Chi-restraints excluded: chain 6 residue 79 LYS Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 120 VAL Chi-restraints excluded: chain 6 residue 204 GLU Chi-restraints excluded: chain 6 residue 209 ASN Chi-restraints excluded: chain 6 residue 210 THR Chi-restraints excluded: chain 6 residue 293 ILE Chi-restraints excluded: chain 6 residue 301 VAL Chi-restraints excluded: chain 6 residue 308 ASN Chi-restraints excluded: chain 6 residue 309 VAL Chi-restraints excluded: chain 5 residue 9 VAL Chi-restraints excluded: chain 5 residue 21 GLU Chi-restraints excluded: chain 5 residue 48 ASP Chi-restraints excluded: chain 5 residue 103 MET Chi-restraints excluded: chain 5 residue 199 ARG Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 227 HIS Chi-restraints excluded: chain 5 residue 255 GLU Chi-restraints excluded: chain 5 residue 269 VAL Chi-restraints excluded: chain 5 residue 272 GLU Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 301 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain c residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 264 optimal weight: 6.9990 chunk 321 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 204 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 300 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 349 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 305 ASN 1 308 ASN 2 206 ASN 2 253 GLN ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN A 302 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN a 52 GLN ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 305 ASN 6 312 GLN ** 6 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.118037 restraints weight = 51052.888| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.56 r_work: 0.3292 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.443 39288 Z= 0.225 Angle : 0.839 29.849 54289 Z= 0.347 Chirality : 0.046 0.201 5375 Planarity : 0.004 0.050 6672 Dihedral : 14.359 179.926 6815 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.75 % Favored : 94.10 % Rotamer: Outliers : 3.61 % Allowed : 19.69 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.13), residues: 3980 helix: 0.23 (0.13), residues: 1415 sheet: -0.36 (0.17), residues: 971 loop : -1.71 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 163 TYR 0.029 0.002 TYR A 599 PHE 0.038 0.002 PHE B 226 TRP 0.020 0.001 TRP C 52 HIS 0.008 0.002 HIS 2 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.22 (39180) covalent geometry : angle 0.80102 / 0.35 (54253) hydrogen bonds : bond 0.04005 / 2.72 ( 1388) hydrogen bonds : angle 5.27054 / 3.77 ( 3972) metal coordination : bond 0.02107 / 1.39 ( 12) metal coordination : angle 9.75493 / 7.19 ( 36) Misc. bond : bond 0.08296 / 6.28 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 420 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 156 ASN cc_start: 0.7981 (m110) cc_final: 0.7769 (m110) REVERT: 3 103 MET cc_start: 0.8174 (ppp) cc_final: 0.7467 (ttm) REVERT: 3 312 GLN cc_start: 0.7857 (tt0) cc_final: 0.7443 (tt0) REVERT: 2 62 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7492 (pptt) REVERT: 2 198 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8581 (mt0) REVERT: 2 200 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8445 (mm) REVERT: 2 238 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8246 (ptm160) REVERT: 2 329 GLN cc_start: 0.8321 (tt0) cc_final: 0.7994 (pt0) REVERT: 2 330 TYR cc_start: 0.8563 (p90) cc_final: 0.8288 (p90) REVERT: A 132 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.5776 (ptpp) REVERT: A 325 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7592 (p90) REVERT: A 352 TYR cc_start: 0.8540 (m-80) cc_final: 0.7872 (m-80) REVERT: A 532 TYR cc_start: 0.8917 (m-80) cc_final: 0.7953 (m-80) REVERT: A 570 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8439 (mtt) REVERT: A 701 ASN cc_start: 0.8434 (t0) cc_final: 0.8169 (t0) REVERT: a 73 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7401 (tp30) REVERT: a 110 ASP cc_start: 0.8041 (m-30) cc_final: 0.7731 (m-30) REVERT: a 163 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7403 (mmm-85) REVERT: a 213 MET cc_start: 0.8264 (mtp) cc_final: 0.8013 (mtt) REVERT: a 222 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8668 (mp) REVERT: a 404 TYR cc_start: 0.8943 (t80) cc_final: 0.8663 (t80) REVERT: 4 85 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: 4 204 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: 4 322 LYS cc_start: 0.7575 (tttt) cc_final: 0.7061 (pmtt) REVERT: 4 339 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7534 (ttm-80) REVERT: 6 204 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6760 (pm20) REVERT: 5 21 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7320 (mt-10) REVERT: 5 199 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7642 (mtm-85) REVERT: F 8 LEU cc_start: 0.7011 (mt) cc_final: 0.6667 (tt) REVERT: F 18 MET cc_start: 0.7870 (mmt) cc_final: 0.7667 (mmt) outliers start: 120 outliers final: 64 residues processed: 501 average time/residue: 0.6467 time to fit residues: 402.0416 Evaluate side-chains 484 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 405 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 301 VAL Chi-restraints excluded: chain 3 residue 11 THR Chi-restraints excluded: chain 3 residue 170 ILE Chi-restraints excluded: chain 3 residue 263 GLN Chi-restraints excluded: chain 3 residue 309 VAL Chi-restraints excluded: chain 2 residue 62 LYS Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 198 GLN Chi-restraints excluded: chain 2 residue 200 ILE Chi-restraints excluded: chain 2 residue 218 VAL Chi-restraints excluded: chain 2 residue 238 ARG Chi-restraints excluded: chain 2 residue 253 GLN Chi-restraints excluded: chain 2 residue 260 SER Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain a residue 55 GLU Chi-restraints excluded: chain a residue 73 GLU Chi-restraints excluded: chain a residue 132 LYS Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 211 VAL Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 470 ILE Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 85 GLU Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 128 ASP Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 4 residue 260 SER Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 278 VAL Chi-restraints excluded: chain 6 residue 49 CYS Chi-restraints excluded: chain 6 residue 79 LYS Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 120 VAL Chi-restraints excluded: chain 6 residue 204 GLU Chi-restraints excluded: chain 6 residue 209 ASN Chi-restraints excluded: chain 6 residue 210 THR Chi-restraints excluded: chain 6 residue 293 ILE Chi-restraints excluded: chain 6 residue 300 MET Chi-restraints excluded: chain 6 residue 301 VAL Chi-restraints excluded: chain 6 residue 308 ASN Chi-restraints excluded: chain 6 residue 309 VAL Chi-restraints excluded: chain 5 residue 9 VAL Chi-restraints excluded: chain 5 residue 21 GLU Chi-restraints excluded: chain 5 residue 48 ASP Chi-restraints excluded: chain 5 residue 103 MET Chi-restraints excluded: chain 5 residue 199 ARG Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 227 HIS Chi-restraints excluded: chain 5 residue 255 GLU Chi-restraints excluded: chain 5 residue 301 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 50 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 393 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 330 optimal weight: 6.9990 chunk 278 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 305 ASN 3 198 GLN 2 206 ASN 2 253 GLN ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN a 52 GLN ** a 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 305 ASN 6 312 GLN ** 6 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 198 GLN ** c 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119947 restraints weight = 51092.717| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.55 r_work: 0.3313 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.455 39288 Z= 0.190 Angle : 0.818 28.982 54289 Z= 0.339 Chirality : 0.045 0.197 5375 Planarity : 0.004 0.049 6672 Dihedral : 14.251 179.940 6815 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.78 % Favored : 94.10 % Rotamer: Outliers : 2.89 % Allowed : 20.56 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 3980 helix: 0.30 (0.13), residues: 1419 sheet: -0.38 (0.17), residues: 970 loop : -1.69 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 163 TYR 0.027 0.002 TYR A 599 PHE 0.034 0.002 PHE B 226 TRP 0.020 0.001 TRP C 52 HIS 0.008 0.002 HIS 2 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (39180) covalent geometry : angle 0.77970 / 0.34 (54253) hydrogen bonds : bond 0.03917 / 2.66 ( 1388) hydrogen bonds : angle 5.21322 / 3.73 ( 3972) metal coordination : bond 0.01791 / 1.19 ( 12) metal coordination : angle 9.66415 / 7.14 ( 36) Misc. bond : bond 0.08142 / 6.23 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 420 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 156 ASN cc_start: 0.7923 (m110) cc_final: 0.7702 (m110) REVERT: 3 103 MET cc_start: 0.8145 (ppp) cc_final: 0.7433 (ttm) REVERT: 3 312 GLN cc_start: 0.7799 (tt0) cc_final: 0.7406 (tt0) REVERT: 2 62 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7516 (pptt) REVERT: 2 198 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8556 (mt0) REVERT: 2 200 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8433 (mm) REVERT: 2 312 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: 2 329 GLN cc_start: 0.8308 (tt0) cc_final: 0.7987 (pt0) REVERT: D 47 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6623 (pt) REVERT: A 132 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.5720 (ptpp) REVERT: A 325 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7586 (p90) REVERT: A 352 TYR cc_start: 0.8485 (m-80) cc_final: 0.7856 (m-80) REVERT: A 436 MET cc_start: 0.8637 (ttp) cc_final: 0.8420 (ttm) REVERT: A 532 TYR cc_start: 0.8889 (m-80) cc_final: 0.7936 (m-80) REVERT: A 701 ASN cc_start: 0.8405 (t0) cc_final: 0.8159 (t0) REVERT: a 73 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: a 110 ASP cc_start: 0.8050 (m-30) cc_final: 0.7724 (m-30) REVERT: a 163 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7451 (mmm-85) REVERT: a 213 MET cc_start: 0.8250 (mtp) cc_final: 0.7941 (mtt) REVERT: a 222 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8632 (mp) REVERT: 4 85 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: 4 204 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: 4 322 LYS cc_start: 0.7590 (tttt) cc_final: 0.7101 (pmtt) REVERT: 4 339 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7509 (ttm-80) REVERT: 6 204 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6754 (pm20) REVERT: 6 337 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: 5 21 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: F 8 LEU cc_start: 0.7001 (mt) cc_final: 0.6668 (tt) REVERT: F 18 MET cc_start: 0.7867 (mmt) cc_final: 0.7648 (mmt) outliers start: 96 outliers final: 63 residues processed: 481 average time/residue: 0.6530 time to fit residues: 391.9968 Evaluate side-chains 485 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 407 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 301 VAL Chi-restraints excluded: chain 3 residue 11 THR Chi-restraints excluded: chain 3 residue 122 LEU Chi-restraints excluded: chain 3 residue 170 ILE Chi-restraints excluded: chain 3 residue 263 GLN Chi-restraints excluded: chain 3 residue 309 VAL Chi-restraints excluded: chain 2 residue 62 LYS Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 2 residue 151 LYS Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 198 GLN Chi-restraints excluded: chain 2 residue 200 ILE Chi-restraints excluded: chain 2 residue 218 VAL Chi-restraints excluded: chain 2 residue 253 GLN Chi-restraints excluded: chain 2 residue 260 SER Chi-restraints excluded: chain 2 residue 312 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain a residue 55 GLU Chi-restraints excluded: chain a residue 73 GLU Chi-restraints excluded: chain a residue 132 LYS Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 211 VAL Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 470 ILE Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 85 GLU Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 4 residue 260 SER Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 278 VAL Chi-restraints excluded: chain 6 residue 14 SER Chi-restraints excluded: chain 6 residue 49 CYS Chi-restraints excluded: chain 6 residue 79 LYS Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 120 VAL Chi-restraints excluded: chain 6 residue 204 GLU Chi-restraints excluded: chain 6 residue 210 THR Chi-restraints excluded: chain 6 residue 293 ILE Chi-restraints excluded: chain 6 residue 301 VAL Chi-restraints excluded: chain 6 residue 308 ASN Chi-restraints excluded: chain 6 residue 309 VAL Chi-restraints excluded: chain 6 residue 337 GLU Chi-restraints excluded: chain 5 residue 9 VAL Chi-restraints excluded: chain 5 residue 21 GLU Chi-restraints excluded: chain 5 residue 48 ASP Chi-restraints excluded: chain 5 residue 103 MET Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 227 HIS Chi-restraints excluded: chain 5 residue 255 GLU Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 301 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 69 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 161 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 228 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 260 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 114 optimal weight: 0.1980 chunk 168 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 305 ASN 2 206 ASN 2 253 GLN D 99 ASN A 302 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN a 52 GLN ** a 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 305 ASN 6 312 GLN ** 6 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119566 restraints weight = 50963.994| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.55 r_work: 0.3311 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.453 39288 Z= 0.200 Angle : 0.825 28.800 54289 Z= 0.342 Chirality : 0.045 0.206 5375 Planarity : 0.004 0.049 6672 Dihedral : 14.185 179.988 6813 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.80 % Favored : 94.10 % Rotamer: Outliers : 2.74 % Allowed : 20.83 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 3980 helix: 0.31 (0.13), residues: 1417 sheet: -0.41 (0.17), residues: 971 loop : -1.66 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 163 TYR 0.026 0.002 TYR A 599 PHE 0.033 0.002 PHE B 226 TRP 0.021 0.001 TRP C 52 HIS 0.008 0.002 HIS 2 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (39180) covalent geometry : angle 0.78626 / 0.34 (54253) hydrogen bonds : bond 0.03917 / 2.66 ( 1388) hydrogen bonds : angle 5.20271 / 3.72 ( 3972) metal coordination : bond 0.01849 / 1.22 ( 12) metal coordination : angle 9.70461 / 7.15 ( 36) Misc. bond : bond 0.08197 / 6.27 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7960 Ramachandran restraints generated. 3980 Oldfield, 0 Emsley, 3980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 420 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 85 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6465 (tm-30) REVERT: 1 101 GLU cc_start: 0.8106 (pp20) cc_final: 0.7834 (pm20) REVERT: 1 156 ASN cc_start: 0.7949 (m110) cc_final: 0.7726 (m110) REVERT: 1 255 GLU cc_start: 0.8035 (tt0) cc_final: 0.7725 (tm-30) REVERT: 3 103 MET cc_start: 0.8158 (ppp) cc_final: 0.7426 (ttm) REVERT: 3 126 ARG cc_start: 0.7000 (mmp-170) cc_final: 0.6716 (tpt170) REVERT: 3 140 MET cc_start: 0.7438 (tpp) cc_final: 0.7237 (tpt) REVERT: 3 312 GLN cc_start: 0.7787 (tt0) cc_final: 0.7369 (tt0) REVERT: 2 62 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7532 (pptt) REVERT: 2 198 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8572 (mt0) REVERT: 2 200 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8380 (mm) REVERT: 2 329 GLN cc_start: 0.8316 (tt0) cc_final: 0.8007 (pt0) REVERT: D 9 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.6329 (mp10) REVERT: A 73 GLU cc_start: 0.8118 (tt0) cc_final: 0.7906 (tt0) REVERT: A 132 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.5774 (ptpp) REVERT: A 325 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7619 (p90) REVERT: A 352 TYR cc_start: 0.8361 (m-80) cc_final: 0.7877 (m-80) REVERT: A 419 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8032 (mt-10) REVERT: A 436 MET cc_start: 0.8636 (ttp) cc_final: 0.8431 (ttm) REVERT: A 532 TYR cc_start: 0.8885 (m-80) cc_final: 0.7888 (m-80) REVERT: A 570 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8429 (mtt) REVERT: A 701 ASN cc_start: 0.8390 (t0) cc_final: 0.8144 (t0) REVERT: a 73 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: a 110 ASP cc_start: 0.8031 (m-30) cc_final: 0.7702 (m-30) REVERT: a 163 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7416 (mmm-85) REVERT: a 213 MET cc_start: 0.8316 (mtp) cc_final: 0.8014 (mtt) REVERT: a 222 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8654 (mp) REVERT: 4 85 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: 4 204 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7870 (pt0) REVERT: 4 322 LYS cc_start: 0.7634 (tttt) cc_final: 0.7193 (pmtt) REVERT: 4 325 TYR cc_start: 0.7806 (t80) cc_final: 0.7600 (t80) REVERT: 4 339 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7609 (ttm-80) REVERT: 6 204 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6747 (pm20) REVERT: 5 15 ASP cc_start: 0.8090 (m-30) cc_final: 0.7849 (m-30) REVERT: 5 21 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: F 8 LEU cc_start: 0.7005 (mt) cc_final: 0.6669 (tt) outliers start: 91 outliers final: 66 residues processed: 479 average time/residue: 0.6394 time to fit residues: 379.9881 Evaluate side-chains 490 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 410 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 97 ILE Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 232 MET Chi-restraints excluded: chain 1 residue 301 VAL Chi-restraints excluded: chain 3 residue 11 THR Chi-restraints excluded: chain 3 residue 122 LEU Chi-restraints excluded: chain 3 residue 170 ILE Chi-restraints excluded: chain 3 residue 263 GLN Chi-restraints excluded: chain 3 residue 309 VAL Chi-restraints excluded: chain 2 residue 62 LYS Chi-restraints excluded: chain 2 residue 110 SER Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 2 residue 151 LYS Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 198 GLN Chi-restraints excluded: chain 2 residue 200 ILE Chi-restraints excluded: chain 2 residue 218 VAL Chi-restraints excluded: chain 2 residue 253 GLN Chi-restraints excluded: chain 2 residue 260 SER Chi-restraints excluded: chain D residue 9 GLN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 302 GLN Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain a residue 55 GLU Chi-restraints excluded: chain a residue 73 GLU Chi-restraints excluded: chain a residue 132 LYS Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 211 VAL Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 470 ILE Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 85 GLU Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 204 GLU Chi-restraints excluded: chain 4 residue 260 SER Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 278 VAL Chi-restraints excluded: chain 6 residue 14 SER Chi-restraints excluded: chain 6 residue 49 CYS Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 120 VAL Chi-restraints excluded: chain 6 residue 204 GLU Chi-restraints excluded: chain 6 residue 209 ASN Chi-restraints excluded: chain 6 residue 210 THR Chi-restraints excluded: chain 6 residue 293 ILE Chi-restraints excluded: chain 6 residue 300 MET Chi-restraints excluded: chain 6 residue 301 VAL Chi-restraints excluded: chain 6 residue 308 ASN Chi-restraints excluded: chain 6 residue 309 VAL Chi-restraints excluded: chain 5 residue 9 VAL Chi-restraints excluded: chain 5 residue 21 GLU Chi-restraints excluded: chain 5 residue 48 ASP Chi-restraints excluded: chain 5 residue 103 MET Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 227 HIS Chi-restraints excluded: chain 5 residue 255 GLU Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 301 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 69 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 180 optimal weight: 0.6980 chunk 316 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 373 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 305 ASN 2 206 ASN 2 253 GLN D 99 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN a 52 GLN ** a 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 305 ASN 6 312 GLN ** 6 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119501 restraints weight = 50914.494| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.55 r_work: 0.3311 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.453 39288 Z= 0.228 Angle : 0.910 59.196 54289 Z= 0.414 Chirality : 0.045 0.367 5375 Planarity : 0.005 0.165 6672 Dihedral : 14.186 179.986 6813 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.80 % Favored : 94.10 % Rotamer: Outliers : 2.80 % Allowed : 21.04 % Favored : 76.16 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 3980 helix: 0.31 (0.13), residues: 1417 sheet: -0.42 (0.17), residues: 971 loop : -1.66 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 163 TYR 0.024 0.002 TYR A 599 PHE 0.029 0.002 PHE B 226 TRP 0.021 0.001 TRP C 52 HIS 0.008 0.002 HIS 2 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (39180) covalent geometry : angle 0.87564 / 0.41 (54253) hydrogen bonds : bond 0.03916 / 2.66 ( 1388) hydrogen bonds : angle 5.20468 / 3.72 ( 3972) metal coordination : bond 0.01816 / 1.20 ( 12) metal coordination : angle 9.70400 / 7.15 ( 36) Misc. bond : bond 0.08193 / 6.27 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12000.78 seconds wall clock time: 205 minutes 47.87 seconds (12347.87 seconds total)