Starting phenix.real_space_refine on Wed Mar 20 21:23:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy8_32196/03_2024/7vy8_32196_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy8_32196/03_2024/7vy8_32196.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy8_32196/03_2024/7vy8_32196_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/7vy8_32196/03_2024/7vy8_32196_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy8_32196/03_2024/7vy8_32196_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy8_32196/03_2024/7vy8_32196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy8_32196/03_2024/7vy8_32196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy8_32196/03_2024/7vy8_32196_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy8_32196/03_2024/7vy8_32196_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= 0.005 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 18081 2.51 5 N 4960 2.21 5 O 5256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G ASP 146": "OD1" <-> "OD2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M GLU 284": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M GLU 410": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P GLU 169": "OE1" <-> "OE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "P GLU 240": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 104": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "Q TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "W TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28527 Number of models: 1 Model: "" Number of chains: 27 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: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 23} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 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: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 47.312 49.216 107.689 1.00 14.92 S ATOM 3060 SG CYS A 425 46.786 46.023 113.585 1.00 19.73 S ATOM 2738 SG CYS A 385 44.161 44.677 107.956 1.00 17.97 S ATOM 2699 SG CYS A 379 42.067 49.723 111.715 1.00 18.05 S ATOM 3961 SG CYS B 113 34.949 63.208 72.674 1.00 6.02 S ATOM 3980 SG CYS B 116 40.306 61.231 76.393 1.00 14.29 S ATOM 4003 SG CYS B 119 41.072 63.709 70.760 1.00 18.24 S ATOM 4332 SG CYS B 162 38.664 57.899 71.746 1.00 9.85 S ATOM 4030 SG CYS B 123 46.900 66.518 65.905 1.00 9.07 S ATOM 4256 SG CYS B 152 45.041 64.452 60.155 1.00 12.92 S ATOM 4303 SG CYS B 158 43.328 60.908 65.363 1.00 17.63 S ATOM 4282 SG CYS B 155 49.309 61.230 63.513 1.00 13.19 S ATOM 5724 SG CYS C 166 51.581 64.482 55.813 1.00 15.46 S ATOM 4996 SG CYS C 72 51.759 65.648 49.485 1.00 14.44 S ATOM 4990 SG CYS C 71 57.254 64.307 52.404 1.00 12.45 S ATOM 5494 SG CYS C 136 53.709 69.507 54.477 1.00 14.43 S ATOM 14949 SG CYS M 131 39.631 61.770 88.414 1.00 17.69 S ATOM 14928 SG CYS M 128 43.272 57.118 85.419 1.00 21.20 S ATOM 14989 SG CYS M 137 45.344 60.869 90.501 1.00 4.24 S ATOM 15321 SG CYS M 179 44.072 61.286 101.501 1.00 10.01 S ATOM 15675 SG CYS M 226 40.785 63.753 97.233 1.00 20.08 S ATOM 15345 SG CYS M 182 38.578 64.027 103.294 1.00 23.47 S ATOM 15298 SG CYS M 176 38.424 58.328 100.159 1.00 11.39 S ATOM 14546 SG CYS M 78 55.718 57.089 105.167 1.00 24.88 S ATOM 14647 SG CYS M 92 53.889 59.237 107.420 1.00 24.18 S ATOM 14435 SG CYS M 64 49.507 59.079 105.336 1.00 6.30 S ATOM 14521 SG CYS M 75 50.579 57.033 102.280 1.00 12.03 S ATOM 21484 SG CYS O 135 31.941 31.680 116.737 1.00 32.00 S ATOM 21518 SG CYS O 140 31.884 28.238 117.984 1.00 42.14 S ATOM 21798 SG CYS O 176 36.345 33.337 119.368 1.00 49.30 S ATOM 21821 SG CYS O 180 36.802 30.038 120.157 1.00 43.28 S ATOM 27631 SG CYS T 86 27.992 50.210 81.212 1.00 17.83 S ATOM 27809 SG CYS T 111 29.217 53.711 81.846 1.00 32.80 S Time building chain proxies: 14.46, per 1000 atoms: 0.51 Number of scatterers: 28527 At special positions: 0 Unit cell: (123.533, 140.72, 164.353, 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 5256 8.00 N 4960 7.00 C 18081 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.71 Conformation dependent library (CDL) restraints added in 4.8 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="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="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " 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="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " 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="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " 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="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " 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=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " 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... running ksdssp... Secondary structure from input PDB file: 150 helices and 26 sheets defined 38.7% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.38 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 71 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.277A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 204 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: 3.719A 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 260 through 264 Processing helix chain 'A' and resid 296 through 302 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 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' 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: 4.386A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.027A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 441 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 77 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 206 removed outlier: 5.627A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 79 removed outlier: 3.718A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) 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 194 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.267A 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: 4.261A 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 39 removed outlier: 5.024A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 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 95 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.039A 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 59 through 61 No H-bonds generated for 'chain 'I' and resid 59 through 61' 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: 4.169A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 5.302A 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 144 No H-bonds generated for 'chain 'J' and resid 141 through 144' Processing helix chain 'J' and resid 147 through 158 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 223 removed outlier: 3.662A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 253 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.989A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 350 through 356 removed outlier: 5.661A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'K' and resid 77 through 80 Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.346A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 69 through 73 removed outlier: 3.933A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.905A 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 128 through 130 No H-bonds generated for 'chain 'M' and resid 128 through 130' Processing helix chain 'M' and resid 134 through 136 No H-bonds generated for 'chain 'M' and resid 134 through 136' 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: 3.540A pdb=" N ILE M 222 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.637A 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 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.526A pdb=" N SER M 332 " --> pdb=" O GLY M 328 " (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 removed outlier: 3.791A pdb=" N ILE M 465 " --> pdb=" O PRO M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 480 through 482 No H-bonds generated for 'chain 'M' and resid 480 through 482' Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 694 Processing helix chain 'M' and resid 699 through 703 Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.610A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 29 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 69 removed outlier: 3.640A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.571A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix removed outlier: 3.914A pdb=" N ASN O 90 " --> pdb=" O GLN O 87 " (cutoff:3.500A) 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 208 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.786A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 5.012A 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: 3.794A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 4.116A 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 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.744A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 139 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: 3.512A pdb=" N TRP Q 202 " --> pdb=" O THR Q 198 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.763A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) 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: 4.659A 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 349 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 433 Processing helix chain 'Q' and resid 435 through 438 No H-bonds generated for 'chain 'Q' and resid 435 through 438' Processing helix chain 'Q' and resid 444 through 454 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 73 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: 7.178A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.282A 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 99 through 103 removed outlier: 4.464A pdb=" N HIS B 101 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 168 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 5.857A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.380A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.420A 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: 7.003A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.835A 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: 6.576A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 229 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= O, first strand: chain 'M' and resid 305 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.524A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.063A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.506A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.541A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.769A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.330A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 77 through 79 Processing sheet with id= Z, first strand: chain 'T' and resid 83 through 86 908 hydrogen bonds defined for protein. 2484 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: 9.01 Time building geometry restraints manager: 11.56 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: 11770 1.40 - 1.62: 17072 1.62 - 1.84: 281 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 29203 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.261 0.263 2.00e-02 2.50e+03 1.72e+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 1.632 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C18 UQ J 402 " pdb=" C19 UQ J 402 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 ... (remaining 29198 not shown) Histogram of bond angle deviations from ideal: 73.59 - 85.96: 76 85.96 - 98.34: 0 98.34 - 110.72: 9490 110.72 - 123.10: 28365 123.10 - 135.48: 1646 Bond angle restraints: 39577 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 107.74 124.25 -16.51 1.95e+00 2.62e-01 7.14e+01 angle pdb=" C HIS M 460 " pdb=" N PRO M 461 " pdb=" CA PRO M 461 " ideal model delta sigma weight residual 119.05 126.99 -7.94 1.11e+00 8.12e-01 5.11e+01 angle pdb=" O1X NDP J 401 " pdb=" P2B NDP J 401 " pdb=" O3X NDP J 401 " ideal model delta sigma weight residual 117.46 109.41 8.05 1.17e+00 7.36e-01 4.77e+01 angle pdb=" C11 CDL I 201 " pdb=" CA5 CDL I 201 " pdb=" OA6 CDL I 201 " ideal model delta sigma weight residual 111.33 119.93 -8.60 1.32e+00 5.72e-01 4.23e+01 angle pdb=" C51 CDL I 201 " pdb=" CB5 CDL I 201 " pdb=" OB6 CDL I 201 " ideal model delta sigma weight residual 111.33 119.92 -8.59 1.32e+00 5.72e-01 4.22e+01 ... (remaining 39572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.33: 16867 31.33 - 62.66: 743 62.66 - 93.99: 63 93.99 - 125.31: 7 125.31 - 156.64: 1 Dihedral angle restraints: 17681 sinusoidal: 7452 harmonic: 10229 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 54.24 -156.64 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" CA LEU I 106 " pdb=" C LEU I 106 " pdb=" N SER I 107 " pdb=" CA SER I 107 " ideal model delta harmonic sigma weight residual 180.00 152.49 27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" C4 PEE C 302 " pdb=" O4P PEE C 302 " pdb=" P PEE C 302 " pdb=" O2P PEE C 302 " ideal model delta sinusoidal sigma weight residual 284.22 158.92 125.30 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 17678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3810 0.071 - 0.143: 460 0.143 - 0.214: 7 0.214 - 0.286: 3 0.286 - 0.357: 3 Chirality restraints: 4283 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 3.19e+00 chirality pdb=" CA CYS A 187 " pdb=" N CYS A 187 " pdb=" C CYS A 187 " pdb=" CB CYS A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C3D NDP J 401 " pdb=" C2D NDP J 401 " pdb=" C4D NDP J 401 " pdb=" O3D NDP J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4280 not shown) Planarity restraints: 5091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " -0.334 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" C13 UQ J 402 " 0.315 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " 0.380 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " -0.003 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " -0.357 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 402 " -0.046 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C11 UQ J 402 " 0.006 2.00e-02 2.50e+03 pdb=" C7 UQ J 402 " -0.306 2.00e-02 2.50e+03 pdb=" C8 UQ J 402 " 0.571 2.00e-02 2.50e+03 pdb=" C9 UQ J 402 " -0.225 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.081 2.00e-02 2.50e+03 2.29e-01 6.54e+02 pdb=" C3N NDP J 401 " 0.401 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.068 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.251 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.164 2.00e-02 2.50e+03 ... (remaining 5088 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 293 2.63 - 3.19: 24553 3.19 - 3.76: 45779 3.76 - 4.33: 67850 4.33 - 4.90: 107068 Nonbonded interactions: 245543 Sorted by model distance: nonbonded pdb=" N SER G 112 " pdb=" O1 8Q1 G 201 " model vdw 2.057 2.496 nonbonded pdb=" N1 FMN A 502 " pdb=" O3' FMN A 502 " model vdw 2.133 2.520 nonbonded pdb=" OG SER J 178 " pdb=" OD2 ASP J 317 " model vdw 2.205 2.440 nonbonded pdb=" OE1 GLU M 81 " pdb=" OG SER M 106 " model vdw 2.207 2.440 nonbonded pdb=" OD1 ASN A 277 " pdb=" OG1 THR A 287 " model vdw 2.209 2.440 ... (remaining 245538 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.180 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 83.010 Find NCS groups from input model: 0.800 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: 0.000 Load rotamer database and sin/cos tables:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 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 0.317 29203 Z= 0.563 Angle : 0.760 16.578 39577 Z= 0.382 Chirality : 0.046 0.357 4283 Planarity : 0.010 0.311 5091 Dihedral : 16.553 156.644 11102 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.20 % Rotamer: Outliers : 0.99 % Allowed : 13.15 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.22 (0.14), residues: 3502 helix: 0.95 (0.14), residues: 1332 sheet: 0.19 (0.26), residues: 376 loop : -0.42 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 PHE 0.017 0.002 PHE Q 204 TYR 0.023 0.002 TYR C 142 ARG 0.014 0.000 ARG H 96 *********************** 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 414 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 384 time to evaluate : 3.286 Fit side-chains revert: symmetry clash REVERT: O 245 VAL cc_start: 0.8985 (p) cc_final: 0.8692 (t) outliers start: 30 outliers final: 22 residues processed: 405 average time/residue: 1.6938 time to fit residues: 781.1618 Evaluate side-chains 397 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 375 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 95 LYS Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 212 GLU Chi-restraints excluded: chain Q residue 217 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 270 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN F 25 GLN F 31 GLN H 73 GLN I 21 GLN I 29 GLN I 51 ASN J 341 GLN M 30 ASN M 464 GLN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 135 GLN P 63 GLN P 123 GLN T 122 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 29203 Z= 0.313 Angle : 0.591 11.964 39577 Z= 0.303 Chirality : 0.045 0.158 4283 Planarity : 0.005 0.078 5091 Dihedral : 10.287 173.049 4174 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 2.56 % Allowed : 12.50 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.17 (0.14), residues: 3502 helix: 0.90 (0.14), residues: 1335 sheet: 0.12 (0.26), residues: 356 loop : -0.42 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 510 HIS 0.007 0.001 HIS T 95 PHE 0.017 0.002 PHE Q 204 TYR 0.022 0.002 TYR P 64 ARG 0.006 0.001 ARG A 269 *********************** 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 459 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 381 time to evaluate : 3.197 Fit side-chains revert: symmetry clash REVERT: A 168 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8977 (m-40) REVERT: C 154 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8661 (p0) REVERT: E 92 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8525 (tt0) REVERT: G 87 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7999 (mp) REVERT: G 146 ASP cc_start: 0.7268 (m-30) cc_final: 0.7024 (m-30) REVERT: I 33 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8634 (mmtm) REVERT: J 234 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: M 108 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8575 (ttmm) REVERT: N 41 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: N 95 ASP cc_start: 0.8864 (m-30) cc_final: 0.8633 (m-30) REVERT: O 245 VAL cc_start: 0.8968 (p) cc_final: 0.8663 (t) REVERT: P 225 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: Q 222 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8694 (mtp) REVERT: T 46 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7959 (m-30) outliers start: 78 outliers final: 39 residues processed: 423 average time/residue: 1.6840 time to fit residues: 813.1439 Evaluate side-chains 425 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 375 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 131 ARG Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 315 GLU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 260 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 339 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 311 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 251 optimal weight: 0.2980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 206 GLN H 73 GLN I 21 GLN I 29 GLN I 51 ASN J 341 GLN M 30 ASN M 464 GLN M 604 GLN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN O 131 HIS P 63 GLN P 123 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29203 Z= 0.276 Angle : 0.565 11.127 39577 Z= 0.290 Chirality : 0.044 0.149 4283 Planarity : 0.005 0.066 5091 Dihedral : 9.864 172.545 4155 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 2.56 % Allowed : 13.35 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.18 (0.14), residues: 3502 helix: 0.91 (0.14), residues: 1340 sheet: 0.12 (0.26), residues: 356 loop : -0.42 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.015 0.002 PHE J 207 TYR 0.020 0.002 TYR P 64 ARG 0.006 0.000 ARG H 96 *********************** 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 463 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 385 time to evaluate : 3.690 Fit side-chains revert: symmetry clash REVERT: B 114 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.8950 (pp) REVERT: C 154 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8590 (p0) REVERT: E 92 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: F 17 ARG cc_start: 0.9266 (mmt-90) cc_final: 0.8792 (mmt180) REVERT: H 7 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5982 (pmmt) REVERT: I 62 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: J 234 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: J 303 ARG cc_start: 0.7747 (tpt170) cc_final: 0.7491 (tpt170) REVERT: K 82 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.8041 (m) REVERT: M 98 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7949 (tptt) REVERT: M 108 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8561 (ttmm) REVERT: M 558 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: N 41 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: N 95 ASP cc_start: 0.8856 (m-30) cc_final: 0.8631 (m-30) REVERT: O 245 VAL cc_start: 0.9037 (p) cc_final: 0.8718 (t) REVERT: P 166 TYR cc_start: 0.9252 (m-80) cc_final: 0.9044 (m-80) REVERT: Q 222 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8681 (mtp) REVERT: Q 308 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.6302 (p90) REVERT: T 46 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7942 (m-30) outliers start: 78 outliers final: 40 residues processed: 425 average time/residue: 1.6842 time to fit residues: 816.0620 Evaluate side-chains 431 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 377 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 558 GLN Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 261 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 315 GLU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 106 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 149 optimal weight: 0.2980 chunk 210 optimal weight: 5.9990 chunk 314 optimal weight: 0.9980 chunk 333 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 298 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN F 31 GLN H 73 GLN I 21 GLN I 51 ASN J 341 GLN M 30 ASN M 464 GLN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN P 63 GLN P 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.0607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29203 Z= 0.254 Angle : 0.548 11.106 39577 Z= 0.282 Chirality : 0.044 0.144 4283 Planarity : 0.005 0.061 5091 Dihedral : 9.561 174.034 4151 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 2.99 % Allowed : 13.32 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.22 (0.14), residues: 3502 helix: 0.96 (0.14), residues: 1339 sheet: 0.10 (0.26), residues: 354 loop : -0.40 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 PHE 0.014 0.002 PHE J 207 TYR 0.019 0.002 TYR P 64 ARG 0.008 0.000 ARG H 96 *********************** 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 481 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 390 time to evaluate : 3.475 Fit side-chains revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: B 114 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.8992 (pp) REVERT: C 154 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8576 (p0) REVERT: E 92 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: F 17 ARG cc_start: 0.9266 (mmt-90) cc_final: 0.8848 (mmt180) REVERT: H 7 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6157 (pmmt) REVERT: I 33 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8632 (mmtm) REVERT: I 70 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7188 (tmt) REVERT: J 85 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8115 (ppt-90) REVERT: J 234 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: J 299 ARG cc_start: 0.7904 (mtp180) cc_final: 0.7551 (mtp85) REVERT: J 303 ARG cc_start: 0.7733 (tpt170) cc_final: 0.7484 (tpt170) REVERT: K 82 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.8042 (m) REVERT: M 98 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7917 (tptt) REVERT: M 108 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8556 (ttmm) REVERT: M 558 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: M 696 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8224 (mtt) REVERT: N 41 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: N 95 ASP cc_start: 0.8843 (m-30) cc_final: 0.8626 (m-30) REVERT: O 245 VAL cc_start: 0.9038 (p) cc_final: 0.8718 (t) REVERT: P 225 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: Q 222 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8642 (mtp) REVERT: Q 308 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.6420 (p90) REVERT: T 46 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7940 (m-30) outliers start: 91 outliers final: 46 residues processed: 436 average time/residue: 1.6742 time to fit residues: 833.1260 Evaluate side-chains 443 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 378 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 50 MET 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 154 ASP Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 558 GLN Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 261 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 315 GLU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 284 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN H 41 ASN H 73 GLN I 21 GLN I 51 ASN J 341 GLN M 30 ASN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 135 GLN P 63 GLN P 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 29203 Z= 0.339 Angle : 0.597 11.356 39577 Z= 0.307 Chirality : 0.046 0.160 4283 Planarity : 0.005 0.062 5091 Dihedral : 9.623 173.432 4151 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.74 % Favored : 96.17 % Rotamer: Outliers : 3.12 % Allowed : 13.61 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.13 (0.14), residues: 3502 helix: 0.84 (0.14), residues: 1340 sheet: 0.12 (0.26), residues: 356 loop : -0.43 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 510 HIS 0.008 0.001 HIS O 131 PHE 0.016 0.002 PHE J 207 TYR 0.022 0.002 TYR J 180 ARG 0.008 0.001 ARG H 96 *********************** 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 482 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 387 time to evaluate : 2.958 Fit side-chains revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: B 114 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9002 (pp) REVERT: C 154 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8651 (p0) REVERT: E 92 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: F 17 ARG cc_start: 0.9309 (mmt-90) cc_final: 0.8896 (mmt180) REVERT: F 46 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7864 (mmtp) REVERT: H 7 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6401 (pmmt) REVERT: H 105 GLU cc_start: 0.8251 (tp30) cc_final: 0.8014 (tp30) REVERT: I 33 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8614 (mmtm) REVERT: I 62 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: J 85 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8266 (ppt-90) REVERT: J 234 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: J 303 ARG cc_start: 0.7715 (tpt170) cc_final: 0.7475 (tpt170) REVERT: K 82 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.8059 (m) REVERT: M 98 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7962 (tptt) REVERT: M 108 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8593 (ttmm) REVERT: M 558 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: M 696 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8333 (mtt) REVERT: N 41 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: N 95 ASP cc_start: 0.8884 (m-30) cc_final: 0.8671 (m-30) REVERT: O 125 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: O 245 VAL cc_start: 0.9061 (p) cc_final: 0.8738 (t) REVERT: P 225 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: Q 137 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8408 (t0) REVERT: Q 222 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8686 (mtp) REVERT: Q 308 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.6443 (p90) REVERT: T 46 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: W 5 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7723 (mmtp) outliers start: 95 outliers final: 50 residues processed: 442 average time/residue: 1.6588 time to fit residues: 837.0363 Evaluate side-chains 454 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 382 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 50 MET 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 154 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG 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 534 VAL Chi-restraints excluded: chain M residue 558 GLN Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 137 ASP Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 261 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 315 GLU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 4.9990 chunk 300 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 333 optimal weight: 0.6980 chunk 277 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 73 GLN I 21 GLN I 51 ASN J 341 GLN M 30 ASN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN P 63 GLN P 123 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29203 Z= 0.163 Angle : 0.506 10.686 39577 Z= 0.259 Chirality : 0.042 0.143 4283 Planarity : 0.004 0.060 5091 Dihedral : 9.147 175.230 4151 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.63 % Rotamer: Outliers : 2.63 % Allowed : 14.40 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.35 (0.14), residues: 3502 helix: 1.12 (0.15), residues: 1325 sheet: -0.02 (0.25), residues: 386 loop : -0.32 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.012 0.001 PHE Q 200 TYR 0.017 0.001 TYR P 64 ARG 0.008 0.000 ARG H 96 *********************** 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 477 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 397 time to evaluate : 3.357 Fit side-chains revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: B 114 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.8949 (pp) REVERT: C 154 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8517 (p0) REVERT: F 17 ARG cc_start: 0.9282 (mmt-90) cc_final: 0.8901 (mmt180) REVERT: F 46 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7770 (mmtp) REVERT: H 7 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6308 (pmmt) REVERT: H 105 GLU cc_start: 0.8230 (tp30) cc_final: 0.8005 (tp30) REVERT: I 33 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8613 (mmtm) REVERT: J 85 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8183 (ppt-90) REVERT: J 234 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: J 303 ARG cc_start: 0.7701 (tpt170) cc_final: 0.7463 (tpt170) REVERT: K 82 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7974 (m) REVERT: M 98 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7847 (tptt) REVERT: M 108 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8504 (ttmm) REVERT: N 47 LYS cc_start: 0.8832 (mttp) cc_final: 0.8529 (mttp) REVERT: O 245 VAL cc_start: 0.9067 (p) cc_final: 0.8748 (t) REVERT: P 225 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: Q 222 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8619 (mtp) REVERT: Q 281 GLU cc_start: 0.8549 (tp30) cc_final: 0.8290 (mp0) REVERT: Q 308 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.6235 (p90) outliers start: 80 outliers final: 38 residues processed: 444 average time/residue: 1.6768 time to fit residues: 847.4041 Evaluate side-chains 438 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 387 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG 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 534 VAL Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 716 GLU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 280 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 332 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN H 73 GLN I 21 GLN I 51 ASN J 341 GLN M 30 ASN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN P 63 GLN P 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29203 Z= 0.246 Angle : 0.544 11.030 39577 Z= 0.279 Chirality : 0.043 0.141 4283 Planarity : 0.005 0.057 5091 Dihedral : 9.142 174.492 4151 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.46 % Rotamer: Outliers : 2.30 % Allowed : 14.76 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.34 (0.14), residues: 3502 helix: 1.06 (0.14), residues: 1328 sheet: 0.17 (0.26), residues: 354 loop : -0.33 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 PHE 0.014 0.001 PHE J 207 TYR 0.019 0.002 TYR J 180 ARG 0.004 0.000 ARG A 269 *********************** 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 460 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 390 time to evaluate : 3.291 Fit side-chains revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: B 114 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.8990 (pp) REVERT: C 154 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8602 (p0) REVERT: F 17 ARG cc_start: 0.9301 (mmt-90) cc_final: 0.8926 (mmt180) REVERT: F 46 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7838 (mmtp) REVERT: H 7 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.6467 (pmmt) REVERT: H 105 GLU cc_start: 0.8241 (tp30) cc_final: 0.8023 (tp30) REVERT: I 33 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8599 (mmtm) REVERT: I 70 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7191 (tmt) REVERT: J 85 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8175 (ppt-90) REVERT: J 234 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: K 82 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7994 (m) REVERT: M 98 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7943 (tptt) REVERT: M 108 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8555 (ttmm) REVERT: M 468 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7166 (mm-30) REVERT: N 41 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7503 (tp30) REVERT: N 47 LYS cc_start: 0.8859 (mttp) cc_final: 0.8500 (mttp) REVERT: N 95 ASP cc_start: 0.8857 (m-30) cc_final: 0.8650 (m-30) REVERT: O 245 VAL cc_start: 0.9057 (p) cc_final: 0.8743 (t) REVERT: P 225 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: Q 222 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8678 (mtp) REVERT: Q 281 GLU cc_start: 0.8563 (tp30) cc_final: 0.8288 (mp0) REVERT: Q 308 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.6292 (p90) outliers start: 70 outliers final: 43 residues processed: 431 average time/residue: 1.7203 time to fit residues: 845.2834 Evaluate side-chains 442 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 384 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 50 MET 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 154 ASP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG 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 534 VAL Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 716 GLU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 100 optimal weight: 0.0980 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN H 73 GLN I 21 GLN I 51 ASN J 341 GLN M 30 ASN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN P 63 GLN P 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 29203 Z= 0.290 Angle : 0.573 11.208 39577 Z= 0.294 Chirality : 0.045 0.151 4283 Planarity : 0.005 0.060 5091 Dihedral : 9.173 173.995 4151 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 2.70 % Allowed : 14.34 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.25 (0.14), residues: 3502 helix: 0.98 (0.14), residues: 1330 sheet: 0.07 (0.26), residues: 358 loop : -0.35 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.015 0.002 PHE J 207 TYR 0.020 0.002 TYR J 180 ARG 0.014 0.000 ARG H 96 *********************** 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 469 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 387 time to evaluate : 3.366 Fit side-chains revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: B 114 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.8974 (pp) REVERT: C 154 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8622 (p0) REVERT: F 17 ARG cc_start: 0.9287 (mmt-90) cc_final: 0.8912 (mmt180) REVERT: G 94 ASP cc_start: 0.5929 (t70) cc_final: 0.5123 (p0) REVERT: H 7 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6483 (pmmt) REVERT: H 105 GLU cc_start: 0.8244 (tp30) cc_final: 0.8031 (tp30) REVERT: I 33 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8604 (mmtm) REVERT: I 70 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7015 (tmt) REVERT: J 85 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8217 (ppt-90) REVERT: J 234 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: K 82 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.8002 (m) REVERT: M 98 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7971 (tptt) REVERT: M 108 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8574 (ttmm) REVERT: M 468 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7200 (mm-30) REVERT: N 41 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7487 (tp30) REVERT: N 47 LYS cc_start: 0.8873 (mttp) cc_final: 0.8509 (mtpp) REVERT: N 95 ASP cc_start: 0.8864 (m-30) cc_final: 0.8652 (m-30) REVERT: O 245 VAL cc_start: 0.9061 (p) cc_final: 0.8755 (t) REVERT: P 225 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: Q 222 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8739 (mtp) REVERT: Q 281 GLU cc_start: 0.8572 (tp30) cc_final: 0.8295 (mp0) REVERT: Q 308 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.6435 (p90) outliers start: 82 outliers final: 46 residues processed: 436 average time/residue: 1.7376 time to fit residues: 860.8359 Evaluate side-chains 444 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 383 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 50 MET 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 154 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 150 ARG 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 534 VAL Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 716 GLU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 315 GLU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 2.9990 chunk 318 optimal weight: 3.9990 chunk 290 optimal weight: 0.5980 chunk 309 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 95 optimal weight: 0.0470 chunk 280 optimal weight: 0.1980 chunk 293 optimal weight: 5.9990 chunk 308 optimal weight: 0.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN H 73 GLN I 51 ASN J 341 GLN M 30 ASN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN P 63 GLN P 123 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29203 Z= 0.144 Angle : 0.495 10.713 39577 Z= 0.253 Chirality : 0.041 0.141 4283 Planarity : 0.004 0.059 5091 Dihedral : 8.707 175.725 4151 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 1.97 % Allowed : 15.00 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.47 (0.14), residues: 3502 helix: 1.23 (0.15), residues: 1320 sheet: 0.09 (0.25), residues: 381 loop : -0.27 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.011 0.001 PHE Q 200 TYR 0.016 0.001 TYR P 64 ARG 0.004 0.000 ARG A 269 *********************** 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 459 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 399 time to evaluate : 3.552 Fit side-chains revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: B 50 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7352 (tpt) REVERT: B 114 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.8896 (pp) REVERT: B 208 ASP cc_start: 0.8547 (t70) cc_final: 0.8322 (t70) REVERT: C 154 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8505 (p0) REVERT: F 17 ARG cc_start: 0.9220 (mmt-90) cc_final: 0.8882 (mmt180) REVERT: G 94 ASP cc_start: 0.6091 (t70) cc_final: 0.5178 (p0) REVERT: I 33 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8597 (mmtm) REVERT: J 85 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8090 (ppt-90) REVERT: J 234 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: K 82 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7952 (m) REVERT: M 468 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7180 (mm-30) REVERT: N 9 ARG cc_start: 0.7144 (ttm110) cc_final: 0.6405 (mtm180) REVERT: N 47 LYS cc_start: 0.8840 (mttp) cc_final: 0.8481 (mttp) REVERT: O 245 VAL cc_start: 0.9064 (p) cc_final: 0.8768 (t) REVERT: P 225 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: Q 222 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8661 (mtp) REVERT: Q 281 GLU cc_start: 0.8543 (tp30) cc_final: 0.8289 (mp0) REVERT: Q 308 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.6229 (p90) outliers start: 60 outliers final: 39 residues processed: 434 average time/residue: 1.7222 time to fit residues: 855.6458 Evaluate side-chains 438 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 388 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 150 ARG 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 534 VAL Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 716 GLU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 154 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 5.9990 chunk 327 optimal weight: 0.6980 chunk 199 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 343 optimal weight: 0.8980 chunk 316 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 73 GLN I 21 GLN I 51 ASN J 341 GLN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN P 63 GLN P 123 GLN T 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29203 Z= 0.167 Angle : 0.506 10.735 39577 Z= 0.258 Chirality : 0.042 0.145 4283 Planarity : 0.004 0.063 5091 Dihedral : 8.598 175.722 4151 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 1.94 % Allowed : 15.19 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.54 (0.14), residues: 3502 helix: 1.29 (0.15), residues: 1318 sheet: 0.13 (0.26), residues: 371 loop : -0.22 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 PHE 0.012 0.001 PHE Q 458 TYR 0.016 0.001 TYR J 180 ARG 0.015 0.000 ARG H 96 ********************** 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 447 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 388 time to evaluate : 3.313 Fit side-chains revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: B 50 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7360 (tpt) REVERT: B 114 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.8907 (pp) REVERT: B 208 ASP cc_start: 0.8557 (t70) cc_final: 0.8302 (t70) REVERT: C 154 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8520 (p0) REVERT: F 17 ARG cc_start: 0.9259 (mmt-90) cc_final: 0.8920 (mmt180) REVERT: G 94 ASP cc_start: 0.6061 (t70) cc_final: 0.5173 (p0) REVERT: I 33 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8600 (mmtm) REVERT: I 70 MET cc_start: 0.7531 (tmt) cc_final: 0.6953 (tmt) REVERT: J 85 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8081 (ppt-90) REVERT: J 234 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: K 82 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7948 (m) REVERT: L 86 ASN cc_start: 0.9120 (OUTLIER) cc_final: 0.8443 (t0) REVERT: M 468 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7193 (mm-30) REVERT: N 9 ARG cc_start: 0.7182 (ttm110) cc_final: 0.6430 (mtm180) REVERT: N 47 LYS cc_start: 0.8821 (mttp) cc_final: 0.8486 (mttp) REVERT: O 245 VAL cc_start: 0.9059 (p) cc_final: 0.8767 (t) REVERT: P 225 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: Q 281 GLU cc_start: 0.8548 (tp30) cc_final: 0.8288 (mp0) REVERT: Q 308 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.6236 (p90) outliers start: 59 outliers final: 42 residues processed: 426 average time/residue: 1.7067 time to fit residues: 839.2133 Evaluate side-chains 437 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 384 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 150 ARG 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 534 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 716 GLU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 3.9990 chunk 291 optimal weight: 0.0970 chunk 83 optimal weight: 0.0770 chunk 252 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 73 GLN I 21 GLN I 51 ASN J 341 GLN M 30 ASN M 666 GLN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 135 GLN P 63 GLN P 123 GLN T 43 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.095081 restraints weight = 34871.246| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.24 r_work: 0.2887 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29203 Z= 0.200 Angle : 0.521 10.905 39577 Z= 0.266 Chirality : 0.042 0.149 4283 Planarity : 0.004 0.058 5091 Dihedral : 8.581 175.340 4151 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 1.91 % Allowed : 15.32 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.49 (0.14), residues: 3502 helix: 1.20 (0.15), residues: 1326 sheet: 0.13 (0.26), residues: 371 loop : -0.23 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.006 0.001 HIS J 37 PHE 0.012 0.001 PHE J 207 TYR 0.017 0.001 TYR J 180 ARG 0.005 0.000 ARG A 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11996.57 seconds wall clock time: 212 minutes 22.91 seconds (12742.91 seconds total)