Starting phenix.real_space_refine on Fri Mar 6 11:29:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vb7_31874/03_2026/7vb7_31874_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vb7_31874/03_2026/7vb7_31874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vb7_31874/03_2026/7vb7_31874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vb7_31874/03_2026/7vb7_31874.map" model { file = "/net/cci-nas-00/data/ceres_data/7vb7_31874/03_2026/7vb7_31874_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vb7_31874/03_2026/7vb7_31874_neut.cif" } resolution = 2.4 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= 0.003 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 Fe 28 7.16 5 Zn 1 6.06 5 P 11 5.49 5 Mg 1 5.21 5 S 189 5.16 5 C 18096 2.51 5 N 4957 2.21 5 O 5996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29279 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3096 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 364} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 212 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 23} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {' UQ': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'DCQ': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "J" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "M" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 196 Classifications: {'water': 196} Link IDs: {None: 195} Chain: "N" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "O" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "Q" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 189 Classifications: {'water': 189} Link IDs: {None: 188} Chain: "T" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 48.556 49.082 105.808 1.00 8.93 S ATOM 3060 SG CYS A 425 47.499 46.092 111.653 1.00 11.64 S ATOM 2738 SG CYS A 385 45.121 44.880 105.671 1.00 10.66 S ATOM 2699 SG CYS A 379 43.088 49.981 109.411 1.00 11.28 S ATOM 3961 SG CYS B 113 39.438 64.023 70.056 1.00 8.63 S ATOM 3980 SG CYS B 116 44.377 61.788 74.194 1.00 7.24 S ATOM 4003 SG CYS B 119 45.707 64.349 68.693 1.00 6.41 S ATOM 4332 SG CYS B 162 43.004 58.591 69.320 1.00 6.59 S ATOM 4030 SG CYS B 123 52.120 66.933 64.479 1.00 5.57 S ATOM 4256 SG CYS B 152 50.545 65.148 58.494 1.00 5.43 S ATOM 4303 SG CYS B 158 48.370 61.508 63.408 1.00 5.61 S ATOM 4282 SG CYS B 155 54.394 61.529 62.271 1.00 5.57 S ATOM 5724 SG CYS C 166 57.314 65.013 54.642 1.00 6.57 S ATOM 4996 SG CYS C 72 58.148 66.196 48.326 1.00 8.24 S ATOM 4990 SG CYS C 71 63.268 64.477 51.590 1.00 8.34 S ATOM 5494 SG CYS C 136 59.936 69.865 53.540 1.00 6.60 S ATOM 14949 SG CYS M 131 42.973 62.176 86.061 1.00 6.82 S ATOM 14928 SG CYS M 128 46.679 57.604 83.300 1.00 6.60 S ATOM 14989 SG CYS M 137 48.651 61.178 88.530 1.00 6.51 S ATOM 15321 SG CYS M 179 45.500 61.778 99.423 1.00 8.52 S ATOM 15675 SG CYS M 226 43.313 64.242 94.985 1.00 7.88 S ATOM 15345 SG CYS M 182 40.710 64.308 100.890 1.00 9.62 S ATOM 15298 SG CYS M 176 40.484 58.749 97.700 1.00 7.38 S ATOM 14546 SG CYS M 78 57.322 56.828 104.024 1.00 8.22 S ATOM 14647 SG CYS M 92 55.469 59.100 106.300 1.00 9.99 S ATOM 14435 SG CYS M 64 51.367 58.893 103.902 1.00 7.47 S ATOM 14521 SG CYS M 75 52.503 56.937 100.800 1.00 6.61 S ATOM 21484 SG CYS O 135 31.831 32.022 113.306 1.00 24.01 S ATOM 21518 SG CYS O 140 31.508 28.762 114.646 1.00 24.93 S ATOM 21798 SG CYS O 176 36.374 33.585 115.775 1.00 23.24 S ATOM 21821 SG CYS O 180 36.476 30.445 117.286 1.00 26.54 S ATOM 27631 SG CYS T 86 31.390 51.061 77.794 1.00 12.46 S ATOM 27809 SG CYS T 111 32.693 54.523 78.780 1.00 13.20 S Time building chain proxies: 6.82, per 1000 atoms: 0.23 Number of scatterers: 29279 At special positions: 0 Unit cell: (127.293, 139.109, 161.13, 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) Zn 1 29.99 Fe 28 26.01 S 189 16.00 P 11 15.00 Mg 1 11.99 O 5996 8.00 N 4957 7.00 C 18096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb=" FES O 301 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 31 sheets defined 46.0% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 94 through 101 removed outlier: 3.672A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.750A pdb=" N GLU A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 149 removed outlier: 3.620A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.795A pdb=" N PHE A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE A 265 " --> pdb=" O TRP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 362 through 378 Processing helix chain 'A' and resid 382 through 402 removed outlier: 4.427A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 removed outlier: 3.998A pdb=" N ILE A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 457 Proline residue: A 434 - end of helix removed outlier: 3.602A pdb=" N ARG A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 63 through 78 removed outlier: 3.516A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 186 through 209 removed outlier: 5.664A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'C' and resid 42 through 61 Processing helix chain 'C' and resid 70 through 81 removed outlier: 3.999A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 169 through 186 Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'E' and resid 24 through 51 removed outlier: 3.671A pdb=" N ALA E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 75 through 95 Processing helix chain 'E' and resid 99 through 105 Processing helix chain 'E' and resid 117 through 125 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 40 through 48 Processing helix chain 'F' and resid 83 through 96 Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 131 through 138 removed outlier: 4.010A pdb=" N LYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU G 138 " --> pdb=" O ASP G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'H' and resid 19 through 36 Processing helix chain 'H' and resid 42 through 62 Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 76 through 98 removed outlier: 3.695A pdb=" N VAL H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 59 through 63 removed outlier: 3.506A pdb=" N ALA I 63 " --> pdb=" O ARG I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 63 through 76 removed outlier: 3.661A pdb=" N ARG J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 98 removed outlier: 3.521A pdb=" N MET J 92 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.514A pdb=" N ILE J 116 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 146 Processing helix chain 'J' and resid 146 through 160 Processing helix chain 'J' and resid 178 through 195 Processing helix chain 'J' and resid 213 through 219 Processing helix chain 'J' and resid 220 through 224 removed outlier: 3.540A pdb=" N PHE J 223 " --> pdb=" O MET J 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 233 Processing helix chain 'J' and resid 242 through 255 Processing helix chain 'J' and resid 256 through 259 removed outlier: 3.828A pdb=" N LYS J 259 " --> pdb=" O PRO J 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 256 through 259' Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 294 through 306 Processing helix chain 'J' and resid 315 through 323 Processing helix chain 'J' and resid 334 through 339 Processing helix chain 'J' and resid 344 through 348 Processing helix chain 'J' and resid 349 through 354 Processing helix chain 'J' and resid 355 through 357 No H-bonds generated for 'chain 'J' and resid 355 through 357' Processing helix chain 'J' and resid 358 through 362 removed outlier: 3.532A pdb=" N LEU J 362 " --> pdb=" O TYR J 359 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 369 removed outlier: 4.032A pdb=" N VAL J 369 " --> pdb=" O MET J 366 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 81 removed outlier: 3.583A pdb=" N TYR K 81 " --> pdb=" O HIS K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 94 Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 69 through 74 Processing helix chain 'L' and resid 130 through 141 Processing helix chain 'L' and resid 160 through 165 removed outlier: 3.564A pdb=" N SER L 165 " --> pdb=" O ALA L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 56 removed outlier: 3.846A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.562A pdb=" N ASN M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 147 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 180 through 189 Processing helix chain 'M' and resid 200 through 204 Processing helix chain 'M' and resid 220 through 226 removed outlier: 4.054A pdb=" N ASP M 224 " --> pdb=" O GLY M 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 245 Processing helix chain 'M' and resid 287 through 293 Processing helix chain 'M' and resid 294 through 299 Processing helix chain 'M' and resid 318 through 333 Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 347 through 361 Processing helix chain 'M' and resid 381 through 386 removed outlier: 3.809A pdb=" N LEU M 386 " --> pdb=" O SER M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 392 through 397 removed outlier: 4.034A pdb=" N GLU M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 411 Processing helix chain 'M' and resid 411 through 425 Processing helix chain 'M' and resid 449 through 457 removed outlier: 4.095A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 468 removed outlier: 3.698A pdb=" N GLN M 464 " --> pdb=" O HIS M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 479 through 484 removed outlier: 5.272A pdb=" N SER M 484 " --> pdb=" O LEU M 481 " (cutoff:3.500A) Processing helix chain 'M' and resid 485 through 504 Processing helix chain 'M' and resid 521 through 529 Processing helix chain 'M' and resid 534 through 540 Processing helix chain 'M' and resid 556 through 560 Processing helix chain 'M' and resid 588 through 592 removed outlier: 4.060A pdb=" N LYS M 592 " --> pdb=" O TYR M 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 630 Processing helix chain 'M' and resid 638 through 650 Processing helix chain 'M' and resid 651 through 655 Processing helix chain 'M' and resid 664 through 673 Processing helix chain 'M' and resid 690 through 694 Processing helix chain 'M' and resid 698 through 703 Processing helix chain 'M' and resid 704 through 716 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 18 through 31 removed outlier: 4.023A pdb=" N GLY N 22 " --> pdb=" O GLY N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 82 Processing helix chain 'N' and resid 83 through 91 Processing helix chain 'O' and resid 56 through 68 Processing helix chain 'O' and resid 74 through 77 Processing helix chain 'O' and resid 78 through 91 Processing helix chain 'O' and resid 94 through 106 Processing helix chain 'O' and resid 108 through 119 removed outlier: 3.619A pdb=" N VAL O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 143 removed outlier: 3.683A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 157 removed outlier: 3.781A pdb=" N ILE O 148 " --> pdb=" O ASN O 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 183 Processing helix chain 'O' and resid 197 through 210 Processing helix chain 'P' and resid 51 through 69 Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 162 through 175 removed outlier: 4.044A pdb=" N TYR P 166 " --> pdb=" O ALA P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 Processing helix chain 'Q' and resid 119 through 125 removed outlier: 3.852A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 133 Processing helix chain 'Q' and resid 133 through 138 removed outlier: 4.025A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 133 through 138' Processing helix chain 'Q' and resid 143 through 160 removed outlier: 3.577A pdb=" N ASN Q 147 " --> pdb=" O SER Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 195 Processing helix chain 'Q' and resid 197 through 219 removed outlier: 4.136A pdb=" N PHE Q 201 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 263 removed outlier: 3.776A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 273 Processing helix chain 'Q' and resid 279 through 286 Processing helix chain 'Q' and resid 290 through 295 Processing helix chain 'Q' and resid 301 through 306 Processing helix chain 'Q' and resid 310 through 314 removed outlier: 3.581A pdb=" N VAL Q 314 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 350 Processing helix chain 'Q' and resid 367 through 372 Processing helix chain 'Q' and resid 374 through 387 Processing helix chain 'Q' and resid 426 through 434 removed outlier: 4.091A pdb=" N ALA Q 430 " --> pdb=" O ALA Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 439 Processing helix chain 'Q' and resid 443 through 455 removed outlier: 3.752A pdb=" N ASP Q 455 " --> pdb=" O ILE Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 463 Processing helix chain 'T' and resid 49 through 56 removed outlier: 3.527A pdb=" N ARG T 52 " --> pdb=" O ASP T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 73 Processing helix chain 'T' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 199 Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 291 Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.473A pdb=" N THR B 129 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B 145 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU B 131 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG B 141 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.328A pdb=" N MET C 103 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N MET C 133 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL C 105 " --> pdb=" O MET C 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 58 removed outlier: 8.584A pdb=" N LEU F 54 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE F 19 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG F 56 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE F 21 " --> pdb=" O ARG F 56 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS F 58 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU F 23 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 67 through 71 removed outlier: 5.239A pdb=" N SER I 71 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLN P 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE P 87 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL P 76 " --> pdb=" O GLU P 85 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU P 85 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU P 133 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU P 111 " --> pdb=" O LEU P 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 103 through 107 removed outlier: 6.557A pdb=" N ALA J 56 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL J 58 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL J 55 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE J 127 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR J 57 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL J 126 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE J 167 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASN J 128 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 206 through 207 Processing sheet with id=AB2, first strand: chain 'J' and resid 226 through 228 removed outlier: 5.825A pdb=" N VAL J 226 " --> pdb=" O TYR J 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AB4, first strand: chain 'L' and resid 125 through 128 Processing sheet with id=AB5, first strand: chain 'L' and resid 106 through 108 Processing sheet with id=AB6, first strand: chain 'M' and resid 39 through 43 removed outlier: 9.236A pdb=" N ILE M 102 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE M 35 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU M 81 " --> pdb=" O LEU M 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AB8, first strand: chain 'M' and resid 196 through 198 Processing sheet with id=AB9, first strand: chain 'M' and resid 246 through 251 removed outlier: 7.763A pdb=" N ASN M 260 " --> pdb=" O PRO M 275 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL M 262 " --> pdb=" O ILE M 273 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE M 273 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER M 264 " --> pdb=" O MET M 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 314 through 316 removed outlier: 6.780A pdb=" N ILE M 566 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU M 584 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR M 568 " --> pdb=" O LEU M 584 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 443 through 446 removed outlier: 6.870A pdb=" N VAL M 429 " --> pdb=" O ASP M 443 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU M 445 " --> pdb=" O VAL M 429 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU M 431 " --> pdb=" O LEU M 445 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE M 400 " --> pdb=" O ALA M 430 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE M 432 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU M 402 " --> pdb=" O ILE M 432 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'M' and resid 595 through 597 Processing sheet with id=AC4, first strand: chain 'N' and resid 37 through 41 removed outlier: 6.769A pdb=" N TYR N 48 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.851A pdb=" N TYR O 192 " --> pdb=" O GLY O 217 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 153 through 154 removed outlier: 6.697A pdb=" N ILE P 153 " --> pdb=" O ALA P 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'P' and resid 208 through 213 Processing sheet with id=AC8, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.380A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AD1, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id=AD2, first strand: chain 'T' and resid 30 through 31 removed outlier: 4.204A pdb=" N ARG T 30 " --> pdb=" O VAL T 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 77 through 78 removed outlier: 5.985A pdb=" N SER T 77 " --> pdb=" O ARG T 119 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 83 through 86 1156 hydrogen bonds defined for protein. 3171 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: 5.40 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 11792 1.40 - 1.62: 17069 1.62 - 1.85: 278 1.85 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 29219 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.262 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.633 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.300 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C18 UQ J 402 " pdb=" C19 UQ J 402 " ideal model delta sigma weight residual 1.336 1.555 -0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 29214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 39272 3.26 - 6.52: 270 6.52 - 9.79: 36 9.79 - 13.05: 13 13.05 - 16.31: 7 Bond angle restraints: 39598 Sorted by residual: angle pdb=" N VAL Q 94 " pdb=" CA VAL Q 94 " pdb=" C VAL Q 94 " ideal model delta sigma weight residual 112.29 119.45 -7.16 9.40e-01 1.13e+00 5.81e+01 angle pdb=" C51 CDL I 201 " pdb=" CB5 CDL I 201 " pdb=" OB6 CDL I 201 " ideal model delta sigma weight residual 111.33 120.66 -9.33 1.32e+00 5.72e-01 4.98e+01 angle pdb=" N GLY M 576 " pdb=" CA GLY M 576 " pdb=" C GLY M 576 " ideal model delta sigma weight residual 112.77 121.08 -8.31 1.28e+00 6.10e-01 4.22e+01 angle pdb=" C11 CDL I 201 " pdb=" CA5 CDL I 201 " pdb=" OA6 CDL I 201 " ideal model delta sigma weight residual 111.33 119.85 -8.52 1.32e+00 5.72e-01 4.16e+01 angle pdb=" N ALA M 397 " pdb=" CA ALA M 397 " pdb=" C ALA M 397 " ideal model delta sigma weight residual 109.96 118.81 -8.85 1.50e+00 4.44e-01 3.48e+01 ... (remaining 39593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 17057 34.20 - 68.41: 589 68.41 - 102.61: 57 102.61 - 136.82: 4 136.82 - 171.02: 6 Dihedral angle restraints: 17713 sinusoidal: 7484 harmonic: 10229 Sorted by residual: dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -128.79 42.79 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CA SER F 59 " pdb=" C SER F 59 " pdb=" N ASP F 60 " pdb=" CA ASP F 60 " ideal model delta harmonic sigma weight residual -180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" C2 PLX C 303 " pdb=" O1 PLX C 303 " pdb=" P1 PLX C 303 " pdb=" O2 PLX C 303 " ideal model delta sinusoidal sigma weight residual 178.46 -10.52 -171.02 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 17710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3803 0.075 - 0.149: 448 0.149 - 0.224: 26 0.224 - 0.298: 3 0.298 - 0.373: 3 Chirality restraints: 4283 Sorted by residual: chirality pdb=" CA THR M 180 " pdb=" N THR M 180 " pdb=" C THR M 180 " pdb=" CB THR M 180 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C6 PLX C 303 " pdb=" C7 PLX C 303 " pdb=" O6 PLX C 303 " pdb=" O7 PLX C 303 " both_signs ideal model delta sigma weight residual False 2.01 2.33 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA TYR Q 141 " pdb=" N TYR Q 141 " pdb=" C TYR Q 141 " pdb=" CB TYR Q 141 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 4280 not shown) Planarity restraints: 5092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 UQ J 402 " -0.522 2.00e-02 2.50e+03 4.47e-01 2.50e+03 pdb=" C23 UQ J 402 " 0.610 2.00e-02 2.50e+03 pdb=" C24 UQ J 402 " 0.417 2.00e-02 2.50e+03 pdb=" C25 UQ J 402 " -0.087 2.00e-02 2.50e+03 pdb=" C26 UQ J 402 " -0.417 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 402 " -0.002 2.00e-02 2.50e+03 3.67e-01 1.68e+03 pdb=" C11 UQ J 402 " -0.406 2.00e-02 2.50e+03 pdb=" C7 UQ J 402 " -0.413 2.00e-02 2.50e+03 pdb=" C8 UQ J 402 " 0.422 2.00e-02 2.50e+03 pdb=" C9 UQ J 402 " 0.399 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.307 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C18 UQ J 402 " 0.569 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " -0.229 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " 0.029 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.062 2.00e-02 2.50e+03 ... (remaining 5089 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 332 2.57 - 3.15: 23455 3.15 - 3.74: 49799 3.74 - 4.32: 74051 4.32 - 4.90: 113296 Nonbonded interactions: 260933 Sorted by model distance: nonbonded pdb=" NH2 ARG I 27 " pdb=" OE1 GLU Q 212 " model vdw 1.988 3.120 nonbonded pdb=" OE2 GLU Q 208 " pdb=" NH2 ARG Q 221 " model vdw 2.089 3.120 nonbonded pdb=" ND2 ASN L 109 " pdb=" O LEU L 111 " model vdw 2.106 3.120 nonbonded pdb=" OD1 ASN Q 147 " pdb=" O HOH Q 601 " model vdw 2.106 3.040 nonbonded pdb=" O PRO Q 89 " pdb=" O HOH Q 602 " model vdw 2.117 3.040 ... (remaining 260928 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 11.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 34.950 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.530 29256 Z= 0.456 Angle : 0.861 23.207 39681 Z= 0.431 Chirality : 0.048 0.373 4283 Planarity : 0.011 0.447 5092 Dihedral : 16.895 171.020 11134 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 1.28 % Allowed : 11.38 % Favored : 87.34 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.70 % 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: 0.48 (0.14), residues: 3502 helix: 0.93 (0.14), residues: 1361 sheet: 0.49 (0.26), residues: 378 loop : -0.11 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 95 TYR 0.018 0.002 TYR P 64 PHE 0.016 0.002 PHE Q 458 TRP 0.015 0.001 TRP P 171 HIS 0.010 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00683 (29219) covalent geometry : angle 0.78441 (39598) SS BOND : bond 0.00887 ( 1) SS BOND : angle 4.85478 ( 2) hydrogen bonds : bond 0.15154 ( 1156) hydrogen bonds : angle 6.34537 ( 3171) metal coordination : bond 0.09000 ( 35) metal coordination : angle 7.84603 ( 81) Misc. bond : bond 0.45637 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 415 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: J 254 LYS cc_start: 0.8048 (mttt) cc_final: 0.7837 (mmtp) REVERT: K 74 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7157 (mmm160) REVERT: M 632 MET cc_start: 0.8157 (ptt) cc_final: 0.7854 (mtm) REVERT: N 142 THR cc_start: 0.7006 (p) cc_final: 0.6653 (t) REVERT: O 150 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6482 (mp0) outliers start: 39 outliers final: 32 residues processed: 442 average time/residue: 0.8408 time to fit residues: 421.9406 Evaluate side-chains 432 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 398 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 306 GLU Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 470 LYS Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain P residue 248 PRO Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 31 GLN H 41 ASN I 29 GLN J 323 HIS M 300 GLN M 334 GLN M 498 GLN N 123 GLN O 106 GLN O 153 GLN O 182 ASN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN P 247 GLN Q 88 HIS ** Q 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.098096 restraints weight = 28292.097| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.01 r_work: 0.2805 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29256 Z= 0.135 Angle : 0.649 19.891 39681 Z= 0.301 Chirality : 0.044 0.157 4283 Planarity : 0.005 0.056 5092 Dihedral : 10.716 149.670 4238 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 1.58 % Allowed : 11.32 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.73 (0.14), residues: 3502 helix: 1.24 (0.14), residues: 1383 sheet: 0.36 (0.25), residues: 384 loop : -0.01 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 95 TYR 0.017 0.001 TYR P 64 PHE 0.020 0.002 PHE Q 458 TRP 0.012 0.001 TRP M 422 HIS 0.008 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00292 (29219) covalent geometry : angle 0.56633 (39598) SS BOND : bond 0.01170 ( 1) SS BOND : angle 4.92791 ( 2) hydrogen bonds : bond 0.05070 ( 1156) hydrogen bonds : angle 5.18027 ( 3171) metal coordination : bond 0.00897 ( 35) metal coordination : angle 7.01192 ( 81) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 414 time to evaluate : 1.254 Fit side-chains REVERT: A 52 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6634 (mtp85) REVERT: A 448 GLU cc_start: 0.8040 (tp30) cc_final: 0.7807 (tm-30) REVERT: C 142 TYR cc_start: 0.9477 (OUTLIER) cc_final: 0.9061 (t80) REVERT: E 30 ARG cc_start: 0.8501 (ttp-170) cc_final: 0.8127 (ttm110) REVERT: F 26 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7323 (mtm-85) REVERT: G 81 ASP cc_start: 0.7336 (m-30) cc_final: 0.6993 (p0) REVERT: G 82 ARG cc_start: 0.7512 (mtm180) cc_final: 0.7024 (mmm-85) REVERT: H 73 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7384 (mm110) REVERT: I 109 ASP cc_start: 0.8575 (t0) cc_final: 0.8355 (t0) REVERT: K 74 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7097 (mmm160) REVERT: L 108 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: M 632 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8277 (mtm) REVERT: M 705 GLN cc_start: 0.8876 (mt0) cc_final: 0.8573 (mm-40) REVERT: N 142 THR cc_start: 0.6942 (p) cc_final: 0.6534 (t) REVERT: O 46 GLU cc_start: 0.7552 (mp0) cc_final: 0.7241 (OUTLIER) REVERT: O 150 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: P 56 LYS cc_start: 0.8995 (mttm) cc_final: 0.8625 (tmtm) outliers start: 48 outliers final: 20 residues processed: 441 average time/residue: 0.8646 time to fit residues: 433.5930 Evaluate side-chains 419 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 394 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 306 GLU Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 450 LYS Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 209 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 255 optimal weight: 20.0000 chunk 308 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 307 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 277 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 48 HIS F 31 GLN H 41 ASN I 25 GLN M 39 GLN M 334 GLN M 498 GLN P 75 GLN P 77 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN Q 92 HIS T 117 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.116345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.092747 restraints weight = 28145.638| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.03 r_work: 0.2743 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 29256 Z= 0.301 Angle : 0.816 20.441 39681 Z= 0.403 Chirality : 0.054 0.226 4283 Planarity : 0.006 0.069 5092 Dihedral : 10.796 146.059 4197 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.52 % Rotamer: Outliers : 3.12 % Allowed : 9.84 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.41 (0.14), residues: 3502 helix: 0.88 (0.14), residues: 1366 sheet: 0.39 (0.26), residues: 358 loop : -0.14 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 83 TYR 0.026 0.003 TYR Q 397 PHE 0.023 0.003 PHE Q 458 TRP 0.021 0.003 TRP P 171 HIS 0.014 0.002 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00711 (29219) covalent geometry : angle 0.75280 (39598) SS BOND : bond 0.01847 ( 1) SS BOND : angle 6.53802 ( 2) hydrogen bonds : bond 0.07108 ( 1156) hydrogen bonds : angle 5.51241 ( 3171) metal coordination : bond 0.01540 ( 35) metal coordination : angle 6.95670 ( 81) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 399 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.6796 (mtp85) REVERT: B 114 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8976 (pp) REVERT: F 26 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7339 (mtm-85) REVERT: G 81 ASP cc_start: 0.7384 (m-30) cc_final: 0.7023 (p0) REVERT: H 22 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7485 (tp30) REVERT: I 70 MET cc_start: 0.8219 (tmt) cc_final: 0.7783 (tmt) REVERT: J 182 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7828 (mtp180) REVERT: J 304 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8266 (tm) REVERT: K 74 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7236 (mmm160) REVERT: L 108 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: M 666 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8337 (tm130) REVERT: M 688 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7301 (mm-40) REVERT: O 46 GLU cc_start: 0.7533 (mp0) cc_final: 0.7210 (OUTLIER) REVERT: O 150 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: P 56 LYS cc_start: 0.9035 (mttm) cc_final: 0.8699 (tmtm) REVERT: P 63 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8446 (tt0) outliers start: 95 outliers final: 46 residues processed: 454 average time/residue: 0.8607 time to fit residues: 443.5164 Evaluate side-chains 454 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 397 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 182 ARG Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 306 GLU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 450 LYS Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 666 GLN Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain O residue 249 LEU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 444 LEU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 107 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 332 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 121 optimal weight: 0.0030 chunk 67 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 45 ASN E 48 HIS F 31 GLN H 41 ASN I 25 GLN K 75 ASN M 498 GLN M 705 GLN P 75 GLN P 77 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.095887 restraints weight = 28104.677| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.04 r_work: 0.2792 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29256 Z= 0.145 Angle : 0.649 19.641 39681 Z= 0.306 Chirality : 0.045 0.160 4283 Planarity : 0.005 0.062 5092 Dihedral : 10.200 143.727 4197 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 2.47 % Allowed : 10.79 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.64 (0.14), residues: 3502 helix: 1.16 (0.14), residues: 1370 sheet: 0.27 (0.25), residues: 383 loop : -0.03 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 95 TYR 0.018 0.002 TYR P 64 PHE 0.020 0.002 PHE Q 458 TRP 0.012 0.001 TRP M 422 HIS 0.010 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00319 (29219) covalent geometry : angle 0.57027 (39598) SS BOND : bond 0.01257 ( 1) SS BOND : angle 5.14953 ( 2) hydrogen bonds : bond 0.05122 ( 1156) hydrogen bonds : angle 5.13973 ( 3171) metal coordination : bond 0.00963 ( 35) metal coordination : angle 6.85188 ( 81) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 403 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.6641 (mtp85) REVERT: A 448 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7612 (tp30) REVERT: B 114 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8923 (pp) REVERT: C 188 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8262 (mtmm) REVERT: E 30 ARG cc_start: 0.8533 (ttp-170) cc_final: 0.8179 (ttm110) REVERT: F 26 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7317 (mtm-85) REVERT: F 46 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7934 (mtpt) REVERT: G 81 ASP cc_start: 0.7366 (m-30) cc_final: 0.6995 (p0) REVERT: H 66 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7766 (mttp) REVERT: I 70 MET cc_start: 0.7898 (tmt) cc_final: 0.7622 (tmt) REVERT: K 74 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7159 (mmm160) REVERT: L 108 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: M 632 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8267 (mtm) REVERT: M 666 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8295 (tm130) REVERT: M 688 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7275 (mm-40) REVERT: N 142 THR cc_start: 0.6936 (p) cc_final: 0.6546 (t) REVERT: O 46 GLU cc_start: 0.7523 (mp0) cc_final: 0.7212 (mp0) REVERT: O 150 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7440 (mp0) outliers start: 75 outliers final: 34 residues processed: 444 average time/residue: 0.8328 time to fit residues: 419.2464 Evaluate side-chains 438 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 393 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 306 GLU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 666 GLN Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 107 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 298 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 333 optimal weight: 8.9990 chunk 324 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 263 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS B 59 GLN E 48 HIS F 31 GLN F 62 GLN H 41 ASN I 25 GLN M 334 GLN M 498 GLN P 75 GLN P 77 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN Q 92 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.116645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.093122 restraints weight = 28069.365| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.04 r_work: 0.2748 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 29256 Z= 0.261 Angle : 0.772 20.336 39681 Z= 0.377 Chirality : 0.052 0.198 4283 Planarity : 0.006 0.068 5092 Dihedral : 10.508 144.562 4196 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 2.80 % Allowed : 10.92 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.42 (0.14), residues: 3502 helix: 0.93 (0.14), residues: 1369 sheet: 0.29 (0.26), residues: 360 loop : -0.15 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 224 TYR 0.024 0.003 TYR Q 397 PHE 0.022 0.003 PHE Q 458 TRP 0.018 0.002 TRP P 171 HIS 0.013 0.002 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00612 (29219) covalent geometry : angle 0.70562 (39598) SS BOND : bond 0.01709 ( 1) SS BOND : angle 6.08887 ( 2) hydrogen bonds : bond 0.06639 ( 1156) hydrogen bonds : angle 5.40300 ( 3171) metal coordination : bond 0.01408 ( 35) metal coordination : angle 6.90835 ( 81) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 396 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.6755 (mtp85) REVERT: A 448 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7644 (tp30) REVERT: B 114 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8957 (pp) REVERT: C 188 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8258 (mtmm) REVERT: F 26 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7329 (mtm-85) REVERT: G 81 ASP cc_start: 0.7346 (m-30) cc_final: 0.6967 (p0) REVERT: H 22 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7448 (tp30) REVERT: I 70 MET cc_start: 0.8205 (tmt) cc_final: 0.7814 (tmt) REVERT: K 74 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7270 (mmm160) REVERT: L 108 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: M 666 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8319 (tm130) REVERT: M 688 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7332 (mm-40) REVERT: N 142 THR cc_start: 0.6985 (p) cc_final: 0.6580 (t) REVERT: O 46 GLU cc_start: 0.7559 (mp0) cc_final: 0.7232 (mp0) REVERT: O 150 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: P 56 LYS cc_start: 0.9012 (mttm) cc_final: 0.8672 (tmtm) REVERT: P 63 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8432 (tt0) REVERT: P 69 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9045 (mp) outliers start: 85 outliers final: 49 residues processed: 447 average time/residue: 0.8497 time to fit residues: 429.8331 Evaluate side-chains 454 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 393 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 450 LYS Chi-restraints excluded: chain M residue 470 LYS Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 666 GLN Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain O residue 249 LEU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 107 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 48 optimal weight: 4.9990 chunk 265 optimal weight: 5.9990 chunk 308 optimal weight: 0.9990 chunk 174 optimal weight: 0.1980 chunk 130 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 304 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 48 HIS F 31 GLN F 62 GLN H 41 ASN I 25 GLN K 75 ASN M 498 GLN P 75 GLN P 77 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.097843 restraints weight = 28023.786| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 0.97 r_work: 0.2833 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29256 Z= 0.112 Angle : 0.612 19.701 39681 Z= 0.280 Chirality : 0.043 0.159 4283 Planarity : 0.004 0.056 5092 Dihedral : 9.617 141.209 4193 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 2.17 % Allowed : 11.61 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.75 (0.14), residues: 3502 helix: 1.31 (0.14), residues: 1372 sheet: 0.23 (0.25), residues: 392 loop : -0.00 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 44 TYR 0.017 0.001 TYR P 64 PHE 0.017 0.001 PHE Q 458 TRP 0.012 0.001 TRP M 422 HIS 0.008 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00237 (29219) covalent geometry : angle 0.52489 (39598) SS BOND : bond 0.01096 ( 1) SS BOND : angle 4.70739 ( 2) hydrogen bonds : bond 0.04355 ( 1156) hydrogen bonds : angle 4.96804 ( 3171) metal coordination : bond 0.00869 ( 35) metal coordination : angle 6.94919 ( 81) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 408 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6664 (mtp85) REVERT: A 448 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 452 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7801 (mm110) REVERT: B 114 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8906 (pp) REVERT: E 30 ARG cc_start: 0.8434 (ttp-170) cc_final: 0.8134 (ttm110) REVERT: F 26 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7307 (mtm-85) REVERT: G 81 ASP cc_start: 0.7368 (m-30) cc_final: 0.7025 (p0) REVERT: G 94 ASP cc_start: 0.6076 (t0) cc_final: 0.5777 (p0) REVERT: H 73 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7388 (mm110) REVERT: I 27 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7645 (ptt-90) REVERT: K 74 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7149 (mmm160) REVERT: L 108 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: M 632 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8214 (mtm) REVERT: M 666 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8262 (tm130) REVERT: M 688 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7237 (mm-40) REVERT: N 142 THR cc_start: 0.6975 (p) cc_final: 0.6602 (t) REVERT: O 46 GLU cc_start: 0.7507 (mp0) cc_final: 0.7176 (mp0) REVERT: O 72 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8167 (mm-30) REVERT: O 150 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: T 34 THR cc_start: 0.7524 (OUTLIER) cc_final: 0.7259 (t) outliers start: 66 outliers final: 29 residues processed: 447 average time/residue: 0.8443 time to fit residues: 428.5795 Evaluate side-chains 431 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 390 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 450 LYS Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 666 GLN Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 107 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 66 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 173 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 309 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 341 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 48 HIS F 62 GLN H 41 ASN I 25 GLN M 334 GLN P 75 GLN P 77 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 180 ASN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.117896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.094181 restraints weight = 28007.836| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.00 r_work: 0.2772 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 29256 Z= 0.201 Angle : 0.708 20.050 39681 Z= 0.339 Chirality : 0.048 0.164 4283 Planarity : 0.005 0.065 5092 Dihedral : 9.953 141.830 4192 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 2.53 % Allowed : 11.35 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.60 (0.14), residues: 3502 helix: 1.15 (0.14), residues: 1376 sheet: 0.26 (0.26), residues: 366 loop : -0.08 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 95 TYR 0.022 0.002 TYR I 28 PHE 0.021 0.002 PHE Q 458 TRP 0.014 0.002 TRP P 171 HIS 0.011 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00467 (29219) covalent geometry : angle 0.63604 (39598) SS BOND : bond 0.01448 ( 1) SS BOND : angle 5.41204 ( 2) hydrogen bonds : bond 0.05853 ( 1156) hydrogen bonds : angle 5.21132 ( 3171) metal coordination : bond 0.01149 ( 35) metal coordination : angle 6.85661 ( 81) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 398 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.6707 (mtp85) REVERT: A 448 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 56 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.7109 (mtp180) REVERT: B 114 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.8945 (pp) REVERT: F 26 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7323 (mtm-85) REVERT: G 81 ASP cc_start: 0.7359 (m-30) cc_final: 0.7000 (p0) REVERT: H 22 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: H 66 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7765 (mttp) REVERT: I 27 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7744 (ptt-90) REVERT: K 74 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7253 (mmm160) REVERT: L 108 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: M 666 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8277 (tm130) REVERT: M 688 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7270 (mm-40) REVERT: N 142 THR cc_start: 0.6968 (p) cc_final: 0.6569 (t) REVERT: O 46 GLU cc_start: 0.7522 (mp0) cc_final: 0.7189 (mp0) REVERT: O 150 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: P 56 LYS cc_start: 0.9004 (mttm) cc_final: 0.8650 (tmtm) REVERT: T 34 THR cc_start: 0.7520 (OUTLIER) cc_final: 0.7207 (t) outliers start: 77 outliers final: 38 residues processed: 443 average time/residue: 0.8431 time to fit residues: 424.8927 Evaluate side-chains 445 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 394 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 450 LYS Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 666 GLN Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 107 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 175 optimal weight: 0.9990 chunk 256 optimal weight: 0.3980 chunk 135 optimal weight: 0.7980 chunk 303 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 318 optimal weight: 0.0970 chunk 235 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 48 HIS F 31 GLN F 62 GLN H 41 ASN I 25 GLN J 122 HIS K 75 ASN M 498 GLN P 75 GLN P 77 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.122627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.100102 restraints weight = 28346.813| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 0.99 r_work: 0.2845 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29256 Z= 0.105 Angle : 0.602 20.292 39681 Z= 0.271 Chirality : 0.042 0.155 4283 Planarity : 0.004 0.054 5092 Dihedral : 9.245 138.175 4192 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.06 % Rotamer: Outliers : 1.71 % Allowed : 12.40 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.14), residues: 3502 helix: 1.43 (0.14), residues: 1368 sheet: 0.23 (0.25), residues: 395 loop : 0.06 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 95 TYR 0.017 0.001 TYR P 64 PHE 0.015 0.001 PHE Q 458 TRP 0.013 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00223 (29219) covalent geometry : angle 0.51191 (39598) SS BOND : bond 0.01027 ( 1) SS BOND : angle 4.46703 ( 2) hydrogen bonds : bond 0.04027 ( 1156) hydrogen bonds : angle 4.84317 ( 3171) metal coordination : bond 0.00828 ( 35) metal coordination : angle 6.99305 ( 81) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 414 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 448 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 452 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7819 (mm-40) REVERT: B 56 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7107 (mtp180) REVERT: B 114 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8891 (pp) REVERT: B 181 GLU cc_start: 0.8832 (mp0) cc_final: 0.8588 (mp0) REVERT: E 30 ARG cc_start: 0.8438 (ttp-170) cc_final: 0.8163 (ttm110) REVERT: F 26 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7352 (mtm-85) REVERT: G 81 ASP cc_start: 0.7376 (m-30) cc_final: 0.7042 (p0) REVERT: G 94 ASP cc_start: 0.6056 (t0) cc_final: 0.5822 (p0) REVERT: H 73 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7352 (mm110) REVERT: I 70 MET cc_start: 0.7497 (tmt) cc_final: 0.7279 (tmt) REVERT: K 74 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7174 (mmm160) REVERT: L 108 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: M 632 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8258 (mtm) REVERT: M 688 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7265 (mm-40) REVERT: N 142 THR cc_start: 0.6996 (p) cc_final: 0.6629 (t) REVERT: O 72 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8183 (mm-30) REVERT: O 146 ASP cc_start: 0.8367 (m-30) cc_final: 0.7770 (m-30) REVERT: O 150 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: O 219 ARG cc_start: 0.8527 (mmt180) cc_final: 0.8316 (mmt180) REVERT: T 34 THR cc_start: 0.7427 (OUTLIER) cc_final: 0.7205 (t) outliers start: 52 outliers final: 29 residues processed: 444 average time/residue: 0.8482 time to fit residues: 428.3017 Evaluate side-chains 433 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 394 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 450 LYS Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 235 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 168 optimal weight: 6.9990 chunk 1 optimal weight: 0.0570 chunk 284 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 102 optimal weight: 0.0060 chunk 251 optimal weight: 0.0020 overall best weight: 0.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS B 59 GLN H 41 ASN I 25 GLN J 150 HIS M 334 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN Q 92 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.125757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.102860 restraints weight = 28314.807| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 0.98 r_work: 0.2904 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29256 Z= 0.095 Angle : 0.582 20.894 39681 Z= 0.256 Chirality : 0.041 0.152 4283 Planarity : 0.004 0.053 5092 Dihedral : 8.661 131.996 4189 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 1.28 % Allowed : 12.99 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.05 (0.14), residues: 3502 helix: 1.65 (0.14), residues: 1368 sheet: 0.30 (0.25), residues: 390 loop : 0.12 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 95 TYR 0.014 0.001 TYR P 64 PHE 0.014 0.001 PHE Q 458 TRP 0.013 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00203 (29219) covalent geometry : angle 0.48672 (39598) SS BOND : bond 0.00818 ( 1) SS BOND : angle 4.14432 ( 2) hydrogen bonds : bond 0.03509 ( 1156) hydrogen bonds : angle 4.61350 ( 3171) metal coordination : bond 0.00721 ( 35) metal coordination : angle 7.05398 ( 81) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 411 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: B 114 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8813 (pp) REVERT: B 181 GLU cc_start: 0.8799 (mp0) cc_final: 0.8578 (mp0) REVERT: C 188 LYS cc_start: 0.8329 (mtmm) cc_final: 0.8076 (pttm) REVERT: E 30 ARG cc_start: 0.8335 (ttp-170) cc_final: 0.8043 (ttm110) REVERT: E 121 LYS cc_start: 0.8717 (mtmm) cc_final: 0.8364 (mtpm) REVERT: F 26 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7272 (mtm-85) REVERT: G 81 ASP cc_start: 0.7307 (m-30) cc_final: 0.6979 (p0) REVERT: J 255 ASP cc_start: 0.8121 (t0) cc_final: 0.7908 (t0) REVERT: J 336 GLU cc_start: 0.7960 (pm20) cc_final: 0.7743 (pm20) REVERT: K 74 ARG cc_start: 0.7871 (mmm-85) cc_final: 0.7116 (mmm160) REVERT: L 108 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: M 632 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8235 (mtm) REVERT: M 688 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7264 (mm-40) REVERT: N 142 THR cc_start: 0.6962 (p) cc_final: 0.6604 (t) REVERT: O 72 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: O 150 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: O 219 ARG cc_start: 0.8485 (mmt180) cc_final: 0.8271 (mmt180) REVERT: P 80 CYS cc_start: 0.8016 (m) cc_final: 0.7754 (p) outliers start: 39 outliers final: 19 residues processed: 434 average time/residue: 0.8393 time to fit residues: 413.7478 Evaluate side-chains 415 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 389 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 450 LYS Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 281 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 337 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 269 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 308 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 48 HIS F 80 ASN H 41 ASN I 25 GLN O 153 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN Q 92 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.123100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.099473 restraints weight = 28063.725| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.00 r_work: 0.2859 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29256 Z= 0.113 Angle : 0.606 19.303 39681 Z= 0.273 Chirality : 0.042 0.153 4283 Planarity : 0.004 0.055 5092 Dihedral : 8.745 129.407 4184 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.88 % Favored : 97.09 % Rotamer: Outliers : 1.15 % Allowed : 13.36 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.14), residues: 3502 helix: 1.61 (0.14), residues: 1372 sheet: 0.31 (0.25), residues: 397 loop : 0.15 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 95 TYR 0.015 0.001 TYR P 64 PHE 0.016 0.001 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00248 (29219) covalent geometry : angle 0.52053 (39598) SS BOND : bond 0.00996 ( 1) SS BOND : angle 4.37052 ( 2) hydrogen bonds : bond 0.04078 ( 1156) hydrogen bonds : angle 4.70587 ( 3171) metal coordination : bond 0.00751 ( 35) metal coordination : angle 6.83354 ( 81) Misc. bond : bond 0.00038 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 390 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7020 (mtp180) REVERT: B 114 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8879 (pp) REVERT: C 188 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8115 (pttm) REVERT: E 30 ARG cc_start: 0.8337 (ttp-170) cc_final: 0.8069 (ttm110) REVERT: F 26 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7292 (mtm-85) REVERT: G 81 ASP cc_start: 0.7315 (m-30) cc_final: 0.6991 (p0) REVERT: J 255 ASP cc_start: 0.8099 (t0) cc_final: 0.7892 (t0) REVERT: K 74 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7122 (mmm160) REVERT: L 108 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: M 632 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8212 (mtm) REVERT: M 666 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8227 (tm130) REVERT: M 688 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7245 (mm-40) REVERT: N 142 THR cc_start: 0.6966 (p) cc_final: 0.6599 (t) REVERT: O 72 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8135 (mm-30) REVERT: O 150 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: P 80 CYS cc_start: 0.8006 (m) cc_final: 0.7671 (p) outliers start: 35 outliers final: 23 residues processed: 411 average time/residue: 0.8609 time to fit residues: 401.3386 Evaluate side-chains 416 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 384 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 450 LYS Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 666 GLN Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain T residue 114 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 149 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 335 optimal weight: 3.9990 chunk 311 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 48 HIS F 80 ASN H 41 ASN I 25 GLN O 153 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN Q 92 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.122569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.099209 restraints weight = 28204.165| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 0.99 r_work: 0.2840 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29256 Z= 0.114 Angle : 0.608 19.584 39681 Z= 0.276 Chirality : 0.043 0.153 4283 Planarity : 0.004 0.054 5092 Dihedral : 8.754 125.795 4184 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.92 % Rotamer: Outliers : 1.28 % Allowed : 13.36 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.03 (0.14), residues: 3502 helix: 1.58 (0.14), residues: 1371 sheet: 0.28 (0.25), residues: 397 loop : 0.15 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 95 TYR 0.016 0.001 TYR P 64 PHE 0.017 0.001 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00249 (29219) covalent geometry : angle 0.52339 (39598) SS BOND : bond 0.00990 ( 1) SS BOND : angle 4.35881 ( 2) hydrogen bonds : bond 0.04217 ( 1156) hydrogen bonds : angle 4.75241 ( 3171) metal coordination : bond 0.00765 ( 35) metal coordination : angle 6.84598 ( 81) Misc. bond : bond 0.00035 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12603.22 seconds wall clock time: 214 minutes 37.87 seconds (12877.87 seconds total)