Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 10:37:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwj_32154/08_2023/7vwj_32154_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwj_32154/08_2023/7vwj_32154.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwj_32154/08_2023/7vwj_32154_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwj_32154/08_2023/7vwj_32154_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwj_32154/08_2023/7vwj_32154_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwj_32154/08_2023/7vwj_32154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwj_32154/08_2023/7vwj_32154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwj_32154/08_2023/7vwj_32154_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwj_32154/08_2023/7vwj_32154_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 188 5.16 5 C 17740 2.51 5 N 4888 2.21 5 O 5891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 88": "NH1" <-> "NH2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "G ASP 111": "OD1" <-> "OD2" Residue "G TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 210": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M GLU 320": "OE1" <-> "OE2" Residue "M GLU 370": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "M ASP 551": "OD1" <-> "OD2" Residue "M GLU 628": "OE1" <-> "OE2" Residue "M GLU 647": "OE1" <-> "OE2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O GLU 226": "OE1" <-> "OE2" Residue "P GLU 215": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 28748 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} 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': 1, 'PTRANS': 9, '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: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} 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: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2359 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} 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: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3044 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 20, 'TRANS': 358} Chain breaks: 1 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: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 5, 'TRANS': 23} 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: "G" 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} 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: "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: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} 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: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} 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: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "M" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 189 Classifications: {'water': 189} Link IDs: {None: 188} Chain: "N" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "Q" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "T" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2706 SG CYS A 382 48.429 48.388 103.805 1.00 16.11 S ATOM 3048 SG CYS A 425 47.504 45.275 109.599 1.00 19.70 S ATOM 2726 SG CYS A 385 45.103 44.079 103.907 1.00 17.82 S ATOM 2687 SG CYS A 379 43.070 49.357 107.612 1.00 19.58 S ATOM 3949 SG CYS B 113 38.673 63.554 68.362 1.00 12.32 S ATOM 3968 SG CYS B 116 43.575 61.092 72.350 1.00 11.19 S ATOM 3991 SG CYS B 119 44.931 63.473 66.706 1.00 9.95 S ATOM 4320 SG CYS B 162 41.960 57.948 67.536 1.00 9.49 S ATOM 4018 SG CYS B 123 51.025 65.886 62.305 1.00 9.90 S ATOM 4244 SG CYS B 152 49.352 64.103 56.411 1.00 12.55 S ATOM 4291 SG CYS B 158 47.084 60.649 61.499 1.00 9.09 S ATOM 4270 SG CYS B 155 53.165 60.389 60.050 1.00 12.84 S ATOM 5712 SG CYS C 166 55.798 63.585 52.496 1.00 13.00 S ATOM 4984 SG CYS C 72 56.883 64.912 46.015 1.00 13.04 S ATOM 4978 SG CYS C 71 60.981 62.570 48.541 1.00 13.21 S ATOM 5482 SG CYS C 136 58.571 68.253 50.965 1.00 10.19 S ATOM 14538 SG CYS M 131 42.636 61.685 84.429 1.00 13.04 S ATOM 14517 SG CYS M 128 46.106 56.820 81.400 1.00 14.08 S ATOM 14578 SG CYS M 137 48.173 60.204 86.586 1.00 10.86 S ATOM 14910 SG CYS M 179 46.354 60.778 97.744 1.00 11.77 S ATOM 15264 SG CYS M 226 43.399 63.500 93.229 1.00 11.55 S ATOM 14934 SG CYS M 182 40.968 63.772 99.240 1.00 14.47 S ATOM 14887 SG CYS M 176 40.552 58.230 95.892 1.00 12.32 S ATOM 14135 SG CYS M 78 57.556 55.662 101.742 1.00 13.12 S ATOM 14236 SG CYS M 92 55.797 57.991 104.006 1.00 15.24 S ATOM 14024 SG CYS M 64 51.465 58.018 101.714 1.00 12.00 S ATOM 14110 SG CYS M 75 52.497 56.057 98.778 1.00 12.54 S ATOM 21073 SG CYS O 135 31.370 32.095 111.852 1.00 39.57 S ATOM 21107 SG CYS O 140 31.270 28.781 113.195 1.00 41.04 S ATOM 21387 SG CYS O 176 35.908 33.524 114.824 1.00 39.29 S ATOM 21410 SG CYS O 180 36.051 30.076 115.485 1.00 44.56 S ATOM 27168 SG CYS T 86 30.372 50.873 76.412 1.00 17.61 S ATOM 27346 SG CYS T 111 31.908 54.310 77.351 1.00 17.92 S Time building chain proxies: 13.83, per 1000 atoms: 0.48 Number of scatterers: 28748 At special positions: 0 Unit cell: (126.219, 138.035, 160.056, 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 188 16.00 P 11 15.00 Mg 1 11.99 O 5891 8.00 N 4888 7.00 C 17740 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.23 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " 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="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb=" SF4 A 501 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " 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=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " 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="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " 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=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " 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 " 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 143 helices and 24 sheets defined 39.2% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.950A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.635A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.506A pdb=" N THR A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.755A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.866A pdb=" N ASP A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 211 removed outlier: 5.880A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.302A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.405A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.785A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'G' and resid 76 through 88 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.949A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 75 removed outlier: 4.084A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.870A 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 113 through 120 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 158 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 212 through 220 removed outlier: 3.547A pdb=" N PHE J 217 " --> pdb=" O PHE J 213 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 317 through 323 Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 345 through 356 removed outlier: 4.574A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 80 Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.414A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 65 No H-bonds generated for 'chain 'L' and resid 62 through 65' Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 131 through 140 Processing helix chain 'L' and resid 160 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.597A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.523A pdb=" N ILE M 222 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' Processing helix chain 'M' and resid 288 through 298 removed outlier: 5.194A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.501A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 392 through 396 Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 481 No H-bonds generated for 'chain 'M' and resid 478 through 481' Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 629 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 654 removed outlier: 3.528A pdb=" N VAL M 654 " --> pdb=" O PRO M 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 651 through 654' Processing helix chain 'M' and resid 665 through 673 removed outlier: 3.636A pdb=" N LYS M 673 " --> pdb=" O ASN M 669 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.668A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 68 Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.633A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.510A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.821A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.737A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 139 Proline residue: Q 134 - end of helix removed outlier: 4.093A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 4.142A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 251 through 262 Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.590A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 350 Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 439 removed outlier: 4.450A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 4.286A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.091A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.059A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.386A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 removed outlier: 6.619A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 7.982A pdb=" N PHE J 263 " --> pdb=" O ALA J 198 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER J 168 " --> pdb=" O PRO J 203 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= I, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= J, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= K, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= L, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= M, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.394A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= O, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.501A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.147A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= R, first strand: chain 'N' and resid 60 through 63 removed outlier: 3.575A pdb=" N GLY N 40 " --> pdb=" O TYR N 48 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.604A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.697A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= V, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.508A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS Q 108 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= X, first strand: chain 'T' and resid 83 through 86 907 hydrogen bonds defined for protein. 2448 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: 9.55 Time building geometry restraints manager: 13.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 11556 1.41 - 1.63: 16771 1.63 - 1.85: 274 1.85 - 2.08: 1 2.08 - 2.30: 80 Bond restraints: 28682 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.263 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.289 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.635 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.302 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" CB7 CDL I 201 " pdb=" OB8 CDL I 201 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 ... (remaining 28677 not shown) Histogram of bond angle deviations from ideal: 73.42 - 85.83: 76 85.83 - 98.24: 0 98.24 - 110.65: 8763 110.65 - 123.06: 28305 123.06 - 135.48: 1708 Bond angle restraints: 38852 Sorted by residual: angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 124.51 -16.77 1.95e+00 2.62e-01 7.37e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.43 -14.59 1.91e+00 2.73e-01 5.80e+01 angle pdb=" C51 CDL I 201 " pdb=" CB5 CDL I 201 " pdb=" OB6 CDL I 201 " ideal model delta sigma weight residual 111.33 120.33 -9.00 1.32e+00 5.72e-01 4.64e+01 angle pdb=" C11 CDL I 201 " pdb=" CA5 CDL I 201 " pdb=" OA6 CDL I 201 " ideal model delta sigma weight residual 111.33 120.28 -8.95 1.32e+00 5.72e-01 4.59e+01 angle pdb=" O1X NDP J 401 " pdb=" P2B NDP J 401 " pdb=" O3X NDP J 401 " ideal model delta sigma weight residual 117.46 109.64 7.82 1.17e+00 7.36e-01 4.50e+01 ... (remaining 38847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 16998 35.91 - 71.81: 272 71.81 - 107.72: 36 107.72 - 143.63: 2 143.63 - 179.54: 1 Dihedral angle restraints: 17309 sinusoidal: 7246 harmonic: 10063 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 77.13 -179.54 1 2.00e+01 2.50e-03 4.80e+01 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 -138.56 52.56 1 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" CA SER O 224 " pdb=" C SER O 224 " pdb=" N CYS O 225 " pdb=" CA CYS O 225 " ideal model delta harmonic sigma weight residual 180.00 152.81 27.19 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 17306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3769 0.072 - 0.144: 435 0.144 - 0.215: 11 0.215 - 0.287: 3 0.287 - 0.359: 2 Chirality restraints: 4220 Sorted by residual: chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C2B NDP J 401 " pdb=" C1B NDP J 401 " pdb=" C3B NDP J 401 " pdb=" O2B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C3D NAI A 503 " pdb=" C2D NAI A 503 " pdb=" C4D NAI A 503 " pdb=" O3D NAI A 503 " both_signs ideal model delta sigma weight residual False -2.71 -2.42 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 4217 not shown) Planarity restraints: 4997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.059 2.00e-02 2.50e+03 2.20e-01 6.08e+02 pdb=" C3N NDP J 401 " 0.396 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.072 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.236 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NDP J 401 " 0.116 2.00e-02 2.50e+03 2.07e-01 4.29e+02 pdb=" C2N NDP J 401 " 0.121 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " 0.122 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.359 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP J 401 " 0.065 2.00e-02 2.50e+03 9.46e-02 8.96e+01 pdb=" C5N NDP J 401 " -0.116 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " 0.117 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.066 2.00e-02 2.50e+03 ... (remaining 4994 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 473 2.55 - 3.14: 22390 3.14 - 3.73: 48418 3.73 - 4.31: 72241 4.31 - 4.90: 113171 Nonbonded interactions: 256693 Sorted by model distance: nonbonded pdb=" O GLY J 208 " pdb=" OD1 ASP J 211 " model vdw 1.965 3.040 nonbonded pdb=" O1N NAI A 503 " pdb=" O HOH A 601 " model vdw 2.012 2.440 nonbonded pdb=" OG1 THR Q 178 " pdb=" OH TYR Q 214 " model vdw 2.096 2.440 nonbonded pdb=" O GLU C 126 " pdb=" OH TYR J 89 " model vdw 2.102 2.440 nonbonded pdb=" OH TYR J 68 " pdb=" OE2 GLU J 210 " model vdw 2.132 2.440 ... (remaining 256688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 6.200 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: 0.030 Extract box with map and model: 26.530 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 80.130 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 : 0.007 0.307 28682 Z= 0.480 Angle : 0.715 16.771 38852 Z= 0.362 Chirality : 0.044 0.359 4220 Planarity : 0.006 0.220 4997 Dihedral : 14.075 179.536 10834 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3439 helix: 1.18 (0.14), residues: 1322 sheet: 0.52 (0.26), residues: 402 loop : -0.09 (0.15), residues: 1715 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 504 time to evaluate : 3.275 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 506 average time/residue: 1.7662 time to fit residues: 1017.7365 Evaluate side-chains 418 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 3.265 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 0.9990 chunk 256 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 265 optimal weight: 0.8980 chunk 102 optimal weight: 0.0970 chunk 161 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 307 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN F 31 GLN F 76 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN H 71 GLN I 9 GLN K 79 HIS ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN W 8 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 28682 Z= 0.175 Angle : 0.518 10.652 38852 Z= 0.266 Chirality : 0.042 0.177 4220 Planarity : 0.005 0.071 4997 Dihedral : 7.919 179.155 3973 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.06 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3439 helix: 1.11 (0.14), residues: 1325 sheet: 0.42 (0.26), residues: 400 loop : -0.09 (0.15), residues: 1714 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 423 time to evaluate : 3.402 Fit side-chains outliers start: 58 outliers final: 21 residues processed: 453 average time/residue: 1.7523 time to fit residues: 908.6704 Evaluate side-chains 432 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 411 time to evaluate : 3.344 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 13 residues processed: 8 average time/residue: 0.9852 time to fit residues: 14.1849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 256 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 308 optimal weight: 5.9990 chunk 333 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 247 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS F 76 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN H 50 GLN H 71 GLN I 9 GLN J 71 ASN K 79 HIS ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 28682 Z= 0.247 Angle : 0.556 10.910 38852 Z= 0.285 Chirality : 0.044 0.189 4220 Planarity : 0.005 0.062 4997 Dihedral : 7.883 177.071 3973 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3439 helix: 1.00 (0.14), residues: 1320 sheet: 0.21 (0.26), residues: 406 loop : -0.14 (0.15), residues: 1713 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 406 time to evaluate : 3.328 Fit side-chains outliers start: 66 outliers final: 36 residues processed: 443 average time/residue: 1.7528 time to fit residues: 889.0780 Evaluate side-chains 432 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 396 time to evaluate : 3.257 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 21 residues processed: 15 average time/residue: 0.9517 time to fit residues: 22.3321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 309 optimal weight: 1.9990 chunk 327 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN A 457 HIS F 31 GLN F 76 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN J 79 GLN K 79 HIS L 86 ASN ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 666 GLN N 52 ASN P 82 ASN Q 160 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 28682 Z= 0.219 Angle : 0.534 10.835 38852 Z= 0.274 Chirality : 0.043 0.183 4220 Planarity : 0.005 0.061 4997 Dihedral : 7.671 177.255 3973 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3439 helix: 0.97 (0.14), residues: 1324 sheet: 0.17 (0.26), residues: 408 loop : -0.18 (0.15), residues: 1707 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 413 time to evaluate : 3.158 Fit side-chains outliers start: 72 outliers final: 39 residues processed: 451 average time/residue: 1.7751 time to fit residues: 919.7958 Evaluate side-chains 436 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 397 time to evaluate : 3.628 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 27 residues processed: 12 average time/residue: 0.9992 time to fit residues: 19.9634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN F 76 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN I 9 GLN K 79 HIS ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN P 228 GLN T 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 28682 Z= 0.385 Angle : 0.642 11.252 38852 Z= 0.330 Chirality : 0.048 0.200 4220 Planarity : 0.006 0.065 4997 Dihedral : 7.966 174.861 3973 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.48 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3439 helix: 0.68 (0.14), residues: 1331 sheet: 0.18 (0.26), residues: 390 loop : -0.33 (0.14), residues: 1718 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 388 time to evaluate : 3.397 Fit side-chains outliers start: 81 outliers final: 47 residues processed: 440 average time/residue: 1.7556 time to fit residues: 885.2380 Evaluate side-chains 427 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 380 time to evaluate : 3.508 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 33 residues processed: 14 average time/residue: 0.6890 time to fit residues: 18.1484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 1.9990 chunk 295 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 327 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 108 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN I 9 GLN K 79 HIS ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN T 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 28682 Z= 0.235 Angle : 0.558 10.896 38852 Z= 0.286 Chirality : 0.044 0.178 4220 Planarity : 0.005 0.067 4997 Dihedral : 7.733 176.330 3973 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3439 helix: 0.80 (0.14), residues: 1322 sheet: 0.06 (0.26), residues: 397 loop : -0.29 (0.15), residues: 1720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 397 time to evaluate : 3.346 Fit side-chains outliers start: 79 outliers final: 47 residues processed: 445 average time/residue: 1.7794 time to fit residues: 904.9452 Evaluate side-chains 431 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 384 time to evaluate : 3.362 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 32 residues processed: 15 average time/residue: 0.7051 time to fit residues: 18.8681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 276 optimal weight: 0.4980 chunk 183 optimal weight: 5.9990 chunk 326 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN F 76 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN I 9 GLN K 79 HIS N 52 ASN T 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 28682 Z= 0.274 Angle : 0.577 11.014 38852 Z= 0.296 Chirality : 0.045 0.181 4220 Planarity : 0.005 0.065 4997 Dihedral : 7.733 175.898 3973 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3439 helix: 0.77 (0.14), residues: 1323 sheet: 0.07 (0.26), residues: 392 loop : -0.31 (0.14), residues: 1724 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 389 time to evaluate : 3.364 Fit side-chains outliers start: 76 outliers final: 48 residues processed: 440 average time/residue: 1.7875 time to fit residues: 902.6777 Evaluate side-chains 427 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 379 time to evaluate : 3.537 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 35 residues processed: 13 average time/residue: 0.6788 time to fit residues: 16.6643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 8.9990 chunk 130 optimal weight: 0.5980 chunk 195 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 207 optimal weight: 7.9990 chunk 222 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN I 9 GLN K 79 HIS N 52 ASN T 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 28682 Z= 0.210 Angle : 0.536 10.792 38852 Z= 0.275 Chirality : 0.043 0.168 4220 Planarity : 0.005 0.065 4997 Dihedral : 7.547 177.004 3973 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3439 helix: 0.85 (0.14), residues: 1324 sheet: 0.11 (0.26), residues: 392 loop : -0.26 (0.15), residues: 1723 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 391 time to evaluate : 3.365 Fit side-chains outliers start: 57 outliers final: 44 residues processed: 435 average time/residue: 1.7883 time to fit residues: 892.2796 Evaluate side-chains 432 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 388 time to evaluate : 3.430 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 36 residues processed: 8 average time/residue: 0.5409 time to fit residues: 11.1046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 0.8980 chunk 313 optimal weight: 5.9990 chunk 285 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 312 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN F 76 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN I 9 GLN K 79 HIS N 52 ASN T 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 28682 Z= 0.363 Angle : 0.629 11.460 38852 Z= 0.323 Chirality : 0.047 0.189 4220 Planarity : 0.005 0.065 4997 Dihedral : 7.784 175.028 3973 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.45 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3439 helix: 0.63 (0.14), residues: 1327 sheet: 0.15 (0.26), residues: 385 loop : -0.39 (0.14), residues: 1727 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 383 time to evaluate : 3.261 Fit side-chains outliers start: 63 outliers final: 46 residues processed: 428 average time/residue: 1.7900 time to fit residues: 875.4237 Evaluate side-chains 424 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 378 time to evaluate : 3.402 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 36 residues processed: 10 average time/residue: 0.7186 time to fit residues: 14.4162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 321 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 152 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 337 optimal weight: 0.0040 chunk 310 optimal weight: 7.9990 chunk 268 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN I 9 GLN K 79 HIS N 52 ASN T 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 28682 Z= 0.186 Angle : 0.533 13.344 38852 Z= 0.273 Chirality : 0.042 0.162 4220 Planarity : 0.005 0.067 4997 Dihedral : 7.442 177.419 3973 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.80 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3439 helix: 0.83 (0.14), residues: 1324 sheet: 0.17 (0.26), residues: 390 loop : -0.29 (0.15), residues: 1725 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 400 time to evaluate : 3.469 Fit side-chains outliers start: 44 outliers final: 40 residues processed: 440 average time/residue: 1.7616 time to fit residues: 894.0628 Evaluate side-chains 424 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 384 time to evaluate : 3.220 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 37 residues processed: 4 average time/residue: 0.7359 time to fit residues: 8.1334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 269 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 276 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN F 76 ASN G 103 HIS H 71 GLN I 9 GLN K 79 HIS N 52 ASN T 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.125680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.101612 restraints weight = 32549.292| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.19 r_work: 0.2918 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 28682 Z= 0.168 Angle : 0.516 12.983 38852 Z= 0.264 Chirality : 0.042 0.206 4220 Planarity : 0.004 0.063 4997 Dihedral : 7.204 178.072 3973 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3439 helix: 0.97 (0.14), residues: 1325 sheet: 0.19 (0.26), residues: 401 loop : -0.20 (0.15), residues: 1713 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13804.11 seconds wall clock time: 245 minutes 16.67 seconds (14716.67 seconds total)