Starting phenix.real_space_refine on Wed Mar 20 22:11:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxp_32186/03_2024/7vxp_32186_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxp_32186/03_2024/7vxp_32186.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxp_32186/03_2024/7vxp_32186_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxp_32186/03_2024/7vxp_32186_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxp_32186/03_2024/7vxp_32186_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxp_32186/03_2024/7vxp_32186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxp_32186/03_2024/7vxp_32186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxp_32186/03_2024/7vxp_32186_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxp_32186/03_2024/7vxp_32186_updated.pdb" } resolution = 2.7 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= 0.004 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 10 5.49 5 Mg 1 5.21 5 S 189 5.16 5 C 18157 2.51 5 N 4951 2.21 5 O 5252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 365": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M GLU 244": "OE1" <-> "OE2" Residue "M GLU 284": "OE1" <-> "OE2" Residue "M GLU 670": "OE1" <-> "OE2" Residue "N PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "P GLU 169": "OE1" <-> "OE2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 148": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "Q GLU 406": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" 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: 28589 Number of models: 1 Model: "" Number of chains: 28 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: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 690 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3096 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 364} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 212 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 23} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "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: "N" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {' UQ': 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 48.172 49.201 110.876 1.00 38.77 S ATOM 3060 SG CYS A 425 47.492 46.073 116.763 1.00 36.60 S ATOM 2738 SG CYS A 385 44.790 44.827 110.990 1.00 40.09 S ATOM 2699 SG CYS A 379 42.958 49.903 114.875 1.00 40.62 S ATOM 3961 SG CYS B 113 35.721 63.936 75.950 1.00 37.70 S ATOM 3980 SG CYS B 116 41.038 61.799 79.626 1.00 42.28 S ATOM 4003 SG CYS B 119 41.850 64.393 74.021 1.00 41.35 S ATOM 4332 SG CYS B 162 39.401 58.590 74.920 1.00 30.85 S ATOM 4030 SG CYS B 123 47.868 67.125 69.187 1.00 40.94 S ATOM 4256 SG CYS B 152 45.882 65.378 63.432 1.00 26.27 S ATOM 4303 SG CYS B 158 44.082 61.544 68.427 1.00 34.59 S ATOM 4282 SG CYS B 155 50.043 61.888 66.768 1.00 37.50 S ATOM 5724 SG CYS C 166 52.267 65.218 58.997 1.00 32.96 S ATOM 4996 SG CYS C 72 52.628 66.597 52.738 1.00 43.95 S ATOM 4990 SG CYS C 71 58.038 65.014 55.586 1.00 38.13 S ATOM 5494 SG CYS C 136 54.755 70.265 57.777 1.00 34.39 S ATOM 14946 SG CYS M 131 40.642 62.308 91.641 1.00 50.79 S ATOM 14925 SG CYS M 128 44.156 57.717 88.504 1.00 35.78 S ATOM 14986 SG CYS M 137 46.299 61.173 93.709 1.00 26.74 S ATOM 15318 SG CYS M 179 44.826 61.569 104.905 1.00 31.19 S ATOM 15672 SG CYS M 226 41.608 64.249 100.542 1.00 46.04 S ATOM 15342 SG CYS M 182 39.377 64.327 106.648 1.00 34.85 S ATOM 15295 SG CYS M 176 39.218 58.760 103.378 1.00 34.13 S ATOM 14543 SG CYS M 78 56.645 57.205 108.323 1.00 35.69 S ATOM 14644 SG CYS M 92 54.845 59.279 110.801 1.00 47.18 S ATOM 14432 SG CYS M 64 50.323 59.150 108.592 1.00 28.24 S ATOM 14518 SG CYS M 75 51.221 57.480 105.835 1.00 32.12 S ATOM 21481 SG CYS O 135 32.327 31.841 119.716 1.00 53.01 S ATOM 21515 SG CYS O 140 32.284 28.417 120.813 1.00 53.05 S ATOM 21795 SG CYS O 176 36.702 33.255 122.174 1.00 68.27 S ATOM 21818 SG CYS O 180 37.396 30.101 123.372 1.00 56.36 S ATOM 27628 SG CYS T 86 28.766 50.741 84.182 1.00 38.22 S ATOM 27806 SG CYS T 111 29.824 54.251 85.181 1.00 43.87 S Time building chain proxies: 14.99, per 1000 atoms: 0.52 Number of scatterers: 28589 At special positions: 0 Unit cell: (124.607, 142.869, 167.575, 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 10 15.00 Mg 1 11.99 O 5252 8.00 N 4951 7.00 C 18157 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: 10.51 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb=" SF4 A 501 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " 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="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " 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="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " 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 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 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: 142 helices and 25 sheets defined 37.9% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.27 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 removed outlier: 3.893A pdb=" N SER A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.509A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.578A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 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 339 through 344 Processing helix chain 'A' and resid 363 through 376 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.331A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.041A 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 78 removed outlier: 3.506A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) 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: 5.542A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 43 through 60 Processing helix chain 'C' and resid 71 through 80 removed outlier: 3.762A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 80 " --> pdb=" O MET C 76 " (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 190 through 194 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.368A 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: 4.334A 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 31 through 39 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 88 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: 3.997A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 75 removed outlier: 4.065A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 5.009A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 120 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 213 through 222 removed outlier: 3.578A pdb=" N PHE J 217 " --> pdb=" O PHE J 213 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (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 284 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.557A 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 350 through 356 removed outlier: 5.643A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 removed outlier: 3.592A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 80' Processing helix chain 'K' and resid 85 through 95 removed outlier: 4.520A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 73 removed outlier: 4.316A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 140 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.971A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 145 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 219 through 225 removed outlier: 3.557A pdb=" N ILE M 222 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 298 removed outlier: 5.362A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.558A pdb=" N SER M 332 " --> pdb=" O GLY M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 361 removed outlier: 3.764A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 392 through 395 removed outlier: 3.657A pdb=" N GLU M 395 " --> pdb=" O ALA M 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 392 through 395' 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: 3.554A pdb=" N ILE M 465 " --> pdb=" O PRO M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 481 Processing helix chain 'M' and resid 486 through 503 Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 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 673 removed outlier: 3.515A pdb=" N LYS M 673 " --> pdb=" O ASN M 669 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 4 through 17 removed outlier: 3.666A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 removed outlier: 3.725A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.353A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.623A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.739A 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 162 through 174 removed outlier: 3.685A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 4.125A 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 Processing helix chain 'Q' and resid 133 through 139 removed outlier: 4.009A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 4.028A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.771A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.865A 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: 4.485A 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 438 removed outlier: 4.520A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) 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 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.232A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 5.853A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.201A 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: 6.502A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.468A 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 57 removed outlier: 6.826A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.786A 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: 6.602A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.812A 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 228 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 200 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 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.457A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.266A 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: 8.183A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.448A 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: 6.527A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.498A 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: 6.620A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.955A 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: 6.701A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU P 83 " --> pdb=" O SER P 79 " (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 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 83 through 86 892 hydrogen bonds defined for protein. 2475 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: 9.75 Time building geometry restraints manager: 11.42 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: 11758 1.40 - 1.62: 17145 1.62 - 1.84: 277 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 29260 Sorted by residual: bond pdb=" C18 UQ J 402 " pdb=" C19 UQ J 402 " ideal model delta sigma weight residual 1.336 1.555 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C18 UQ Q 501 " pdb=" C19 UQ Q 501 " ideal model delta sigma weight residual 1.336 1.554 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C13 UQ Q 501 " pdb=" C14 UQ Q 501 " ideal model delta sigma weight residual 1.335 1.547 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C13 UQ J 402 " pdb=" C14 UQ J 402 " ideal model delta sigma weight residual 1.335 1.545 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C8 UQ J 402 " pdb=" C9 UQ J 402 " ideal model delta sigma weight residual 1.334 1.543 -0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 29255 not shown) Histogram of bond angle deviations from ideal: 73.63 - 85.80: 76 85.80 - 97.97: 0 97.97 - 110.14: 5293 110.14 - 122.32: 29914 122.32 - 134.49: 4348 Bond angle restraints: 39631 Sorted by residual: angle pdb=" C GLU J 311 " pdb=" N PRO J 312 " pdb=" CA PRO J 312 " ideal model delta sigma weight residual 119.76 128.63 -8.87 1.00e+00 1.00e+00 7.86e+01 angle pdb=" N MET Q 197 " pdb=" CA MET Q 197 " pdb=" C MET Q 197 " ideal model delta sigma weight residual 111.36 120.68 -9.32 1.09e+00 8.42e-01 7.31e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.94 -16.20 1.95e+00 2.62e-01 6.88e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.25 -13.41 1.91e+00 2.73e-01 4.90e+01 angle pdb=" C SER J 308 " pdb=" N PRO J 309 " pdb=" CA PRO J 309 " ideal model delta sigma weight residual 119.05 126.71 -7.66 1.11e+00 8.12e-01 4.76e+01 ... (remaining 39626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 17129 35.92 - 71.85: 521 71.85 - 107.77: 29 107.77 - 143.70: 1 143.70 - 179.62: 4 Dihedral angle restraints: 17684 sinusoidal: 7455 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 77.21 -179.62 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -139.48 53.48 1 1.00e+01 1.00e-02 3.89e+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 180.00 156.41 23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 17681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3831 0.074 - 0.147: 415 0.147 - 0.221: 21 0.221 - 0.294: 5 0.294 - 0.368: 6 Chirality restraints: 4278 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 -2.38 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA PHE Q 136 " pdb=" N PHE Q 136 " pdb=" C PHE Q 136 " pdb=" CB PHE Q 136 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA THR Q 198 " pdb=" N THR Q 198 " pdb=" C THR Q 198 " pdb=" CB THR Q 198 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 4275 not shown) Planarity restraints: 5097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.468 2.00e-02 2.50e+03 4.09e-01 2.10e+03 pdb=" C18 UQ J 402 " 0.519 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " 0.410 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " -0.035 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ Q 501 " 0.308 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" C18 UQ Q 501 " -0.583 2.00e-02 2.50e+03 pdb=" C19 UQ Q 501 " 0.238 2.00e-02 2.50e+03 pdb=" C20 UQ Q 501 " 0.022 2.00e-02 2.50e+03 pdb=" C21 UQ Q 501 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " 0.311 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C13 UQ J 402 " -0.570 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " 0.218 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " 0.068 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " -0.027 2.00e-02 2.50e+03 ... (remaining 5094 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1126 2.72 - 3.26: 28026 3.26 - 3.81: 47102 3.81 - 4.35: 61825 4.35 - 4.90: 102683 Nonbonded interactions: 240762 Sorted by model distance: nonbonded pdb=" OD2 ASP M 295 " pdb=" OG1 THR M 706 " model vdw 2.172 2.440 nonbonded pdb=" OH TYR Q 226 " pdb=" O GLN Q 234 " model vdw 2.189 2.440 nonbonded pdb=" OG SER B 94 " pdb=" OE2 GLU Q 215 " model vdw 2.203 2.440 nonbonded pdb=" OD1 ASP B 165 " pdb=" NH2 ARG Q 368 " model vdw 2.207 2.520 nonbonded pdb=" OG1 THR Q 178 " pdb=" OH TYR Q 214 " model vdw 2.221 2.440 ... (remaining 240757 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.730 Check model and map are aligned: 0.400 Set scattering table: 0.270 Process input model: 82.410 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 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 0.316 29260 Z= 0.522 Angle : 0.819 16.494 39631 Z= 0.416 Chirality : 0.047 0.368 4278 Planarity : 0.015 0.409 5097 Dihedral : 16.355 179.621 11105 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 1.18 % Allowed : 13.20 % Favored : 85.62 % 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: -0.00 (0.14), residues: 3502 helix: 0.84 (0.14), residues: 1344 sheet: 0.09 (0.26), residues: 386 loop : -0.63 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.005 0.001 HIS Q 223 PHE 0.015 0.001 PHE Q 204 TYR 0.019 0.001 TYR C 142 ARG 0.013 0.000 ARG A 52 *********************** 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 428 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 392 time to evaluate : 2.970 Fit side-chains revert: symmetry clash REVERT: A 456 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7818 (tm-30) REVERT: E 87 LYS cc_start: 0.8816 (mttp) cc_final: 0.8499 (mmmt) REVERT: G 97 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6600 (tptt) REVERT: G 125 GLU cc_start: 0.7140 (tp30) cc_final: 0.6867 (tp30) REVERT: M 441 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7565 (ttp-110) REVERT: N 116 ASN cc_start: 0.8522 (t0) cc_final: 0.8204 (t0) REVERT: Q 145 MET cc_start: 0.9127 (mtt) cc_final: 0.8904 (tpp) REVERT: Q 148 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8507 (pt0) outliers start: 36 outliers final: 28 residues processed: 420 average time/residue: 1.5957 time to fit residues: 768.1602 Evaluate side-chains 410 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 380 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 246 SER Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 457 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 313 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 GLN A 451 GLN F 25 GLN F 62 GLN G 101 ASN H 50 GLN L 109 ASN M 464 GLN M 652 ASN O 69 ASN O 153 GLN P 51 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.0524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 29260 Z= 0.344 Angle : 0.582 10.758 39631 Z= 0.297 Chirality : 0.046 0.184 4278 Planarity : 0.005 0.070 5097 Dihedral : 10.815 177.018 4203 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.14 % Favored : 95.80 % Rotamer: Outliers : 2.70 % Allowed : 12.57 % Favored : 84.73 % 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: -0.08 (0.14), residues: 3502 helix: 0.77 (0.14), residues: 1350 sheet: 0.07 (0.26), residues: 389 loop : -0.68 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 422 HIS 0.005 0.001 HIS Q 223 PHE 0.019 0.002 PHE Q 204 TYR 0.022 0.002 TYR P 64 ARG 0.006 0.000 ARG A 52 *********************** 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 477 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 395 time to evaluate : 3.610 Fit side-chains revert: symmetry clash REVERT: A 456 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 43 MET cc_start: 0.7795 (tpp) cc_final: 0.7562 (tpp) REVERT: C 171 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: E 29 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8021 (mmmt) REVERT: E 87 LYS cc_start: 0.8885 (mttp) cc_final: 0.8543 (mmmt) REVERT: F 95 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8265 (mp) REVERT: G 125 GLU cc_start: 0.7230 (tp30) cc_final: 0.6918 (tp30) REVERT: J 278 GLN cc_start: 0.9145 (tt0) cc_final: 0.8895 (tt0) REVERT: J 311 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: M 42 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8281 (mmm) REVERT: M 150 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7930 (mtp85) REVERT: M 249 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8566 (mt-10) REVERT: M 370 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: M 441 ARG cc_start: 0.7993 (mtp-110) cc_final: 0.7628 (ttp-110) REVERT: M 498 GLN cc_start: 0.8422 (tt0) cc_final: 0.7870 (tp-100) REVERT: M 507 THR cc_start: 0.4409 (OUTLIER) cc_final: 0.4036 (m) REVERT: M 530 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.7960 (t80) REVERT: N 133 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8483 (mmtm) REVERT: O 138 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9070 (p) REVERT: Q 308 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8160 (p90) REVERT: T 43 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8884 (tm-30) REVERT: T 105 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6998 (tp30) REVERT: T 107 LYS cc_start: 0.8450 (tttp) cc_final: 0.7999 (ttpm) outliers start: 82 outliers final: 39 residues processed: 441 average time/residue: 1.6162 time to fit residues: 817.3275 Evaluate side-chains 440 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 386 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 660 GLU Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 208 LEU Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 105 GLU 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: 0.0770 chunk 97 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 213 optimal weight: 0.3980 chunk 86 optimal weight: 6.9990 chunk 313 optimal weight: 3.9990 chunk 339 optimal weight: 5.9990 chunk 279 optimal weight: 0.8980 chunk 311 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 251 optimal weight: 6.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN F 25 GLN F 62 GLN G 101 ASN H 50 GLN M 464 GLN M 558 GLN M 666 GLN O 69 ASN O 153 GLN P 51 ASN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29260 Z= 0.148 Angle : 0.484 10.775 39631 Z= 0.248 Chirality : 0.041 0.212 4278 Planarity : 0.004 0.064 5097 Dihedral : 9.995 179.710 4172 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 2.17 % Allowed : 13.85 % Favored : 83.97 % 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: 0.22 (0.14), residues: 3502 helix: 1.12 (0.15), residues: 1332 sheet: 0.06 (0.25), residues: 410 loop : -0.55 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.003 0.001 HIS J 37 PHE 0.019 0.001 PHE G 126 TYR 0.016 0.001 TYR P 64 ARG 0.009 0.000 ARG A 52 *********************** 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 471 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 405 time to evaluate : 3.106 Fit side-chains revert: symmetry clash REVERT: A 359 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7824 (mtm110) REVERT: A 456 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7814 (tm-30) REVERT: C 171 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: E 87 LYS cc_start: 0.8816 (mttp) cc_final: 0.8497 (mmmt) REVERT: F 45 LYS cc_start: 0.8641 (tptp) cc_final: 0.8347 (tppt) REVERT: F 90 THR cc_start: 0.8963 (t) cc_final: 0.8739 (p) REVERT: F 93 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7356 (t0) REVERT: F 95 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8245 (mp) REVERT: H 30 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8681 (ttpt) REVERT: J 278 GLN cc_start: 0.9089 (tt0) cc_final: 0.8775 (tt0) REVERT: J 311 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7687 (pm20) REVERT: L 78 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8521 (ttt-90) REVERT: M 249 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8494 (mt-10) REVERT: M 441 ARG cc_start: 0.7911 (mtp-110) cc_final: 0.7561 (ttp-110) REVERT: M 498 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7854 (tp-100) REVERT: M 507 THR cc_start: 0.4386 (OUTLIER) cc_final: 0.4035 (m) REVERT: M 530 TYR cc_start: 0.9108 (OUTLIER) cc_final: 0.8045 (t80) REVERT: M 666 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7378 (tm-30) REVERT: N 41 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: O 138 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9068 (p) REVERT: P 50 ARG cc_start: 0.8134 (ttm170) cc_final: 0.7732 (mmt90) REVERT: Q 308 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8012 (p90) REVERT: T 43 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8873 (tm-30) REVERT: T 107 LYS cc_start: 0.8386 (tttp) cc_final: 0.7924 (ttpm) outliers start: 66 outliers final: 26 residues processed: 450 average time/residue: 1.5593 time to fit residues: 804.8462 Evaluate side-chains 430 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 390 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 46 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 210 optimal weight: 0.0870 chunk 314 optimal weight: 4.9990 chunk 333 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 62 GLN G 101 ASN H 50 GLN L 109 ASN M 464 GLN O 69 ASN O 153 GLN P 51 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29260 Z= 0.287 Angle : 0.540 11.040 39631 Z= 0.277 Chirality : 0.044 0.199 4278 Planarity : 0.005 0.065 5097 Dihedral : 9.822 177.539 4157 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.86 % Rotamer: Outliers : 2.47 % Allowed : 14.02 % Favored : 83.51 % 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: 0.10 (0.14), residues: 3502 helix: 0.96 (0.14), residues: 1338 sheet: 0.17 (0.26), residues: 393 loop : -0.61 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.005 0.001 HIS T 95 PHE 0.016 0.002 PHE O 223 TYR 0.019 0.002 TYR P 64 ARG 0.009 0.000 ARG A 52 *********************** 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 470 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 395 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7980 (pttp) REVERT: A 359 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7910 (mtm110) REVERT: A 456 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7843 (tm-30) REVERT: C 171 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: E 87 LYS cc_start: 0.8900 (mttp) cc_final: 0.8511 (mmmt) REVERT: F 45 LYS cc_start: 0.8750 (tptp) cc_final: 0.8483 (tppt) REVERT: F 95 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8250 (mp) REVERT: G 139 MET cc_start: 0.8098 (mmp) cc_final: 0.7835 (tpt) REVERT: H 30 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8695 (ttpt) REVERT: J 212 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.8144 (ttp-170) REVERT: J 311 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: L 78 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8574 (ttt-90) REVERT: M 42 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8183 (mmm) REVERT: M 249 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8577 (mt-10) REVERT: M 370 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: M 441 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7574 (ttp-110) REVERT: M 498 GLN cc_start: 0.8417 (tt0) cc_final: 0.7852 (tp-100) REVERT: M 507 THR cc_start: 0.4419 (OUTLIER) cc_final: 0.4065 (m) REVERT: M 509 ASP cc_start: 0.7516 (p0) cc_final: 0.7283 (p0) REVERT: M 530 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.8080 (t80) REVERT: M 632 MET cc_start: 0.8248 (ptp) cc_final: 0.7982 (mtm) REVERT: M 666 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7477 (tm-30) REVERT: N 133 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8442 (mmtm) REVERT: P 50 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7791 (mmt90) REVERT: P 56 LYS cc_start: 0.8598 (mttm) cc_final: 0.8386 (mtmm) REVERT: P 161 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8381 (mptt) REVERT: Q 308 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8185 (p90) REVERT: Q 323 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8131 (mmm160) REVERT: Q 351 MET cc_start: 0.8949 (tpp) cc_final: 0.8707 (tpp) REVERT: T 43 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8864 (tm-30) REVERT: T 107 LYS cc_start: 0.8422 (tttp) cc_final: 0.7927 (ttpm) outliers start: 75 outliers final: 37 residues processed: 436 average time/residue: 1.5676 time to fit residues: 787.7563 Evaluate side-chains 437 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 383 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 208 LEU Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 46 ASP 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: 0.6980 chunk 189 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 62 GLN G 101 ASN H 50 GLN L 109 ASN M 464 GLN M 558 GLN O 87 GLN O 153 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29260 Z= 0.195 Angle : 0.502 10.806 39631 Z= 0.257 Chirality : 0.042 0.239 4278 Planarity : 0.004 0.065 5097 Dihedral : 9.672 179.900 4157 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 2.70 % Allowed : 14.48 % Favored : 82.82 % 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: 0.21 (0.14), residues: 3502 helix: 1.09 (0.15), residues: 1333 sheet: 0.11 (0.25), residues: 408 loop : -0.55 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.004 0.001 HIS T 95 PHE 0.019 0.001 PHE G 126 TYR 0.017 0.001 TYR P 64 ARG 0.010 0.000 ARG A 52 *********************** 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 480 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 398 time to evaluate : 3.305 Fit side-chains revert: symmetry clash REVERT: A 359 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7869 (mtm110) REVERT: A 456 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7840 (tm-30) REVERT: B 43 MET cc_start: 0.7719 (tpp) cc_final: 0.7516 (tpp) REVERT: B 50 MET cc_start: 0.7627 (tpp) cc_final: 0.7402 (tpt) REVERT: C 171 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: E 87 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8484 (mmmt) REVERT: F 93 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7349 (t0) REVERT: F 95 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8080 (mp) REVERT: G 94 ASP cc_start: 0.6410 (OUTLIER) cc_final: 0.6132 (t70) REVERT: G 97 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6834 (tptt) REVERT: H 30 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8693 (ttpt) REVERT: J 212 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8135 (ttp-170) REVERT: J 261 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8914 (mtmm) REVERT: J 311 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: L 78 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8546 (ttt-90) REVERT: L 112 MET cc_start: 0.8365 (mmm) cc_final: 0.8105 (mmm) REVERT: M 42 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8154 (mmm) REVERT: M 173 MET cc_start: 0.9613 (OUTLIER) cc_final: 0.9365 (mmm) REVERT: M 249 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8537 (mt-10) REVERT: M 370 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8185 (mm-30) REVERT: M 441 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7519 (ttp-110) REVERT: M 498 GLN cc_start: 0.8360 (tt0) cc_final: 0.7849 (tp-100) REVERT: M 507 THR cc_start: 0.4476 (OUTLIER) cc_final: 0.4144 (m) REVERT: M 509 ASP cc_start: 0.7628 (p0) cc_final: 0.7399 (p0) REVERT: M 530 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8051 (t80) REVERT: M 632 MET cc_start: 0.8125 (ptp) cc_final: 0.7848 (mtm) REVERT: M 666 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7407 (tm-30) REVERT: N 133 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8457 (mmtm) REVERT: P 50 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7734 (mmt90) REVERT: P 56 LYS cc_start: 0.8600 (mttm) cc_final: 0.8365 (mtmm) REVERT: Q 308 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8130 (p90) REVERT: Q 323 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8118 (mmm160) REVERT: T 43 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8848 (tm-30) REVERT: T 107 LYS cc_start: 0.8420 (tttp) cc_final: 0.7891 (ttpm) outliers start: 82 outliers final: 35 residues processed: 450 average time/residue: 1.6086 time to fit residues: 837.7649 Evaluate side-chains 440 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 384 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 261 LYS Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 173 MET Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 46 ASP 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: 2.9990 chunk 300 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 333 optimal weight: 3.9990 chunk 277 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 62 GLN G 101 ASN H 50 GLN M 464 GLN O 153 GLN P 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29260 Z= 0.278 Angle : 0.536 10.869 39631 Z= 0.274 Chirality : 0.044 0.239 4278 Planarity : 0.005 0.063 5097 Dihedral : 9.619 178.008 4157 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.75 % Rotamer: Outliers : 2.70 % Allowed : 14.68 % Favored : 82.63 % 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: 0.10 (0.14), residues: 3502 helix: 0.99 (0.14), residues: 1341 sheet: 0.11 (0.25), residues: 398 loop : -0.62 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.004 0.001 HIS T 95 PHE 0.016 0.002 PHE G 126 TYR 0.019 0.001 TYR P 64 ARG 0.011 0.000 ARG A 52 *********************** 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 470 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 388 time to evaluate : 3.337 Fit side-chains revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8020 (pttp) REVERT: A 359 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7897 (mtm110) REVERT: A 456 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7923 (tm-30) REVERT: B 50 MET cc_start: 0.7635 (tpp) cc_final: 0.7417 (tpt) REVERT: C 171 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: E 87 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8485 (mmmt) REVERT: F 95 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8096 (mp) REVERT: G 94 ASP cc_start: 0.6440 (OUTLIER) cc_final: 0.6203 (t70) REVERT: G 97 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7304 (tmmm) REVERT: J 212 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.8179 (ttp-170) REVERT: J 311 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: L 78 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8560 (ttt-90) REVERT: M 42 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8170 (mmm) REVERT: M 75 CYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8534 (p) REVERT: M 249 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8569 (mt-10) REVERT: M 370 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8193 (mm-30) REVERT: M 441 ARG cc_start: 0.7937 (mtp-110) cc_final: 0.7619 (ttp-110) REVERT: M 507 THR cc_start: 0.4241 (OUTLIER) cc_final: 0.3935 (m) REVERT: M 509 ASP cc_start: 0.7654 (p0) cc_final: 0.7410 (p0) REVERT: M 530 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8081 (t80) REVERT: M 632 MET cc_start: 0.8238 (ptp) cc_final: 0.7965 (mtm) REVERT: M 666 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7414 (tm-30) REVERT: N 133 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8440 (mmtm) REVERT: P 56 LYS cc_start: 0.8610 (mttm) cc_final: 0.8370 (mtmm) REVERT: P 161 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8395 (mptt) REVERT: Q 308 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8181 (p90) REVERT: Q 323 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8114 (mmm160) REVERT: Q 351 MET cc_start: 0.8942 (tpp) cc_final: 0.8739 (tpp) REVERT: T 43 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8861 (tm-30) REVERT: T 107 LYS cc_start: 0.8425 (tttp) cc_final: 0.7906 (ttpm) outliers start: 82 outliers final: 40 residues processed: 438 average time/residue: 1.5534 time to fit residues: 781.3700 Evaluate side-chains 439 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 379 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 46 ASP 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: 3.9990 chunk 37 optimal weight: 0.0010 chunk 190 optimal weight: 0.4980 chunk 243 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 280 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 332 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 62 GLN G 101 ASN H 50 GLN I 47 HIS M 464 GLN M 540 ASN M 558 GLN M 598 ASN O 153 GLN P 82 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29260 Z= 0.164 Angle : 0.492 10.846 39631 Z= 0.251 Chirality : 0.041 0.282 4278 Planarity : 0.004 0.063 5097 Dihedral : 9.293 179.888 4157 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 2.50 % Allowed : 15.37 % Favored : 82.13 % 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: 0.30 (0.14), residues: 3502 helix: 1.18 (0.15), residues: 1338 sheet: 0.12 (0.26), residues: 408 loop : -0.51 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.003 0.001 HIS Q 381 PHE 0.017 0.001 PHE G 126 TYR 0.016 0.001 TYR P 64 ARG 0.011 0.000 ARG A 52 *********************** 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 470 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 394 time to evaluate : 3.153 Fit side-chains revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7947 (pttp) REVERT: A 359 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7856 (mtm110) REVERT: A 456 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7919 (tm-30) REVERT: B 146 ASP cc_start: 0.9122 (m-30) cc_final: 0.8880 (m-30) REVERT: C 171 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: E 87 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8514 (mmmt) REVERT: F 93 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7423 (t0) REVERT: F 95 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8180 (mp) REVERT: G 94 ASP cc_start: 0.6377 (OUTLIER) cc_final: 0.6169 (t70) REVERT: G 139 MET cc_start: 0.8123 (mmp) cc_final: 0.7882 (tpt) REVERT: J 212 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8175 (ttp-170) REVERT: J 311 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: L 112 MET cc_start: 0.8444 (mtp) cc_final: 0.8134 (mmm) REVERT: M 42 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8122 (mmm) REVERT: M 75 CYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8521 (p) REVERT: M 173 MET cc_start: 0.9659 (OUTLIER) cc_final: 0.9344 (mmm) REVERT: M 249 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8489 (mt-10) REVERT: M 329 MET cc_start: 0.8541 (mmt) cc_final: 0.8326 (mmm) REVERT: M 441 ARG cc_start: 0.7900 (mtp-110) cc_final: 0.7590 (ttp-110) REVERT: M 507 THR cc_start: 0.4312 (OUTLIER) cc_final: 0.4010 (m) REVERT: M 509 ASP cc_start: 0.7619 (p0) cc_final: 0.7379 (p0) REVERT: M 530 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8003 (t80) REVERT: M 632 MET cc_start: 0.8103 (ptp) cc_final: 0.7831 (mtm) REVERT: M 666 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7373 (tm-30) REVERT: N 41 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: P 56 LYS cc_start: 0.8596 (mttm) cc_final: 0.8344 (mtmm) REVERT: Q 308 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8009 (p90) REVERT: T 43 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8859 (tm-30) REVERT: T 107 LYS cc_start: 0.8387 (tttp) cc_final: 0.7857 (ttpm) outliers start: 76 outliers final: 39 residues processed: 442 average time/residue: 1.5386 time to fit residues: 784.9101 Evaluate side-chains 441 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 385 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 363 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 L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 173 MET Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 46 ASP 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: 4.9990 chunk 132 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 62 GLN G 101 ASN H 50 GLN M 464 GLN O 153 GLN P 51 ASN T 74 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29260 Z= 0.285 Angle : 0.550 10.974 39631 Z= 0.280 Chirality : 0.044 0.282 4278 Planarity : 0.005 0.063 5097 Dihedral : 9.297 178.312 4157 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 2.57 % Allowed : 15.43 % Favored : 82.00 % 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: 0.18 (0.14), residues: 3502 helix: 1.05 (0.14), residues: 1335 sheet: 0.14 (0.26), residues: 398 loop : -0.57 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 510 HIS 0.005 0.001 HIS T 95 PHE 0.017 0.002 PHE G 126 TYR 0.018 0.002 TYR P 64 ARG 0.012 0.000 ARG A 52 *********************** 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 464 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 386 time to evaluate : 3.099 Fit side-chains revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8022 (pttp) REVERT: A 359 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7896 (mtm110) REVERT: A 456 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7934 (tm-30) REVERT: B 43 MET cc_start: 0.7759 (tpp) cc_final: 0.7522 (tpp) REVERT: C 171 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: E 87 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8534 (mmmt) REVERT: F 93 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7356 (t0) REVERT: F 95 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8128 (mp) REVERT: G 94 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.6107 (t70) REVERT: G 122 MET cc_start: 0.8457 (mmm) cc_final: 0.8237 (mmt) REVERT: G 139 MET cc_start: 0.8124 (mmp) cc_final: 0.7817 (tpt) REVERT: H 30 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8696 (ttpt) REVERT: J 212 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8203 (ttp-170) REVERT: J 311 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: L 78 ARG cc_start: 0.8902 (ttt-90) cc_final: 0.8686 (ttp-170) REVERT: M 42 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8153 (mmm) REVERT: M 75 CYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8533 (p) REVERT: M 370 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8127 (mm-30) REVERT: M 441 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7593 (ttp-110) REVERT: M 509 ASP cc_start: 0.7682 (p0) cc_final: 0.7451 (p0) REVERT: M 530 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8089 (t80) REVERT: M 632 MET cc_start: 0.8256 (ptp) cc_final: 0.7975 (mtm) REVERT: M 666 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7392 (tm-30) REVERT: N 133 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8439 (mmtm) REVERT: P 56 LYS cc_start: 0.8609 (mttm) cc_final: 0.8339 (mtmm) REVERT: Q 308 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8114 (p90) REVERT: Q 323 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8111 (mmm160) REVERT: T 43 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8863 (tm-30) REVERT: T 107 LYS cc_start: 0.8403 (tttp) cc_final: 0.7854 (ttpm) outliers start: 78 outliers final: 47 residues processed: 432 average time/residue: 1.5506 time to fit residues: 770.6602 Evaluate side-chains 443 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 379 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 363 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 L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 46 ASP 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: 0.0970 chunk 318 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 309 optimal weight: 0.9980 chunk 186 optimal weight: 0.2980 chunk 134 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 280 optimal weight: 1.9990 chunk 293 optimal weight: 0.0370 chunk 308 optimal weight: 0.8980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN F 25 GLN F 62 GLN G 101 ASN H 50 GLN M 464 GLN M 558 GLN O 153 GLN P 51 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29260 Z= 0.145 Angle : 0.487 11.134 39631 Z= 0.247 Chirality : 0.041 0.289 4278 Planarity : 0.004 0.062 5097 Dihedral : 8.853 178.914 4157 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 1.88 % Allowed : 16.03 % Favored : 82.10 % 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: 0.38 (0.14), residues: 3502 helix: 1.27 (0.15), residues: 1336 sheet: 0.19 (0.26), residues: 416 loop : -0.48 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.003 0.001 HIS T 95 PHE 0.012 0.001 PHE G 126 TYR 0.016 0.001 TYR J 180 ARG 0.010 0.000 ARG A 52 *********************** 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 452 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 395 time to evaluate : 3.120 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7319 (t0) cc_final: 0.7104 (t0) REVERT: A 104 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7966 (pttp) REVERT: A 359 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7839 (mtm110) REVERT: A 456 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 146 ASP cc_start: 0.9103 (m-30) cc_final: 0.8902 (m-30) REVERT: E 87 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8512 (mmmt) REVERT: F 95 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8177 (mp) REVERT: I 64 MET cc_start: 0.8526 (pmt) cc_final: 0.8075 (pmt) REVERT: I 103 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.8090 (mtm180) REVERT: J 212 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.8176 (ttp-170) REVERT: J 311 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: L 78 ARG cc_start: 0.8876 (ttt-90) cc_final: 0.8669 (ttp-170) REVERT: L 112 MET cc_start: 0.8253 (mtp) cc_final: 0.7974 (mmm) REVERT: M 42 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8085 (mmm) REVERT: M 329 MET cc_start: 0.8535 (mmt) cc_final: 0.8318 (mmm) REVERT: M 441 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7575 (ttp-110) REVERT: M 507 THR cc_start: 0.4204 (OUTLIER) cc_final: 0.3900 (m) REVERT: M 509 ASP cc_start: 0.7634 (p0) cc_final: 0.7391 (p0) REVERT: M 530 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8065 (t80) REVERT: M 632 MET cc_start: 0.8034 (ptp) cc_final: 0.7770 (mtm) REVERT: P 56 LYS cc_start: 0.8591 (mttm) cc_final: 0.8323 (mtmm) REVERT: Q 308 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.7978 (p90) REVERT: Q 323 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8042 (mmm160) REVERT: Q 356 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8869 (pt) REVERT: T 43 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8858 (tm-30) REVERT: T 106 THR cc_start: 0.8452 (p) cc_final: 0.8235 (t) REVERT: T 107 LYS cc_start: 0.8375 (tttp) cc_final: 0.7838 (ttpm) outliers start: 57 outliers final: 35 residues processed: 432 average time/residue: 1.5656 time to fit residues: 782.9892 Evaluate side-chains 437 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 390 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 363 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 L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 46 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 4.9990 chunk 327 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 227 optimal weight: 0.4980 chunk 343 optimal weight: 0.0970 chunk 316 optimal weight: 0.9990 chunk 273 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 62 GLN G 101 ASN M 464 GLN O 153 GLN P 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29260 Z= 0.169 Angle : 0.496 12.972 39631 Z= 0.251 Chirality : 0.042 0.279 4278 Planarity : 0.004 0.061 5097 Dihedral : 8.730 179.406 4157 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 1.84 % Allowed : 16.39 % Favored : 81.77 % 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: 0.40 (0.14), residues: 3502 helix: 1.27 (0.15), residues: 1342 sheet: 0.24 (0.26), residues: 414 loop : -0.48 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.003 0.001 HIS Q 381 PHE 0.013 0.001 PHE Q 458 TYR 0.016 0.001 TYR P 64 ARG 0.011 0.000 ARG A 52 ********************** 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 450 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 394 time to evaluate : 3.351 Fit side-chains revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7983 (pttp) REVERT: A 149 MET cc_start: 0.9029 (mtt) cc_final: 0.8478 (mtt) REVERT: A 359 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7846 (mtm110) REVERT: A 456 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7931 (tm-30) REVERT: E 87 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8553 (mmmt) REVERT: F 95 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8162 (mp) REVERT: G 139 MET cc_start: 0.8087 (mmp) cc_final: 0.7854 (tpt) REVERT: I 64 MET cc_start: 0.8439 (pmt) cc_final: 0.8002 (pmt) REVERT: I 103 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8100 (mtm180) REVERT: J 37 HIS cc_start: 0.5572 (t70) cc_final: 0.5115 (t70) REVERT: J 212 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8181 (ttp-170) REVERT: J 311 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: L 78 ARG cc_start: 0.8870 (ttt-90) cc_final: 0.8662 (ttp-170) REVERT: M 42 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8107 (mmm) REVERT: M 75 CYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8514 (p) REVERT: M 329 MET cc_start: 0.8545 (mmt) cc_final: 0.8325 (mmm) REVERT: M 441 ARG cc_start: 0.7875 (mtp-110) cc_final: 0.7560 (ttp-110) REVERT: M 509 ASP cc_start: 0.7668 (p0) cc_final: 0.7409 (p0) REVERT: M 530 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8069 (t80) REVERT: M 632 MET cc_start: 0.8087 (ptp) cc_final: 0.7825 (mtm) REVERT: M 666 GLN cc_start: 0.7767 (tm-30) cc_final: 0.7292 (tm-30) REVERT: N 41 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: N 133 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8417 (mmtm) REVERT: P 56 LYS cc_start: 0.8592 (mttm) cc_final: 0.8328 (mtmm) REVERT: Q 308 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8002 (p90) REVERT: Q 323 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8031 (mmm160) REVERT: Q 356 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8871 (pt) REVERT: T 43 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8853 (tm-30) REVERT: T 106 THR cc_start: 0.8430 (p) cc_final: 0.8222 (t) REVERT: T 107 LYS cc_start: 0.8340 (tttp) cc_final: 0.7818 (ttpm) outliers start: 56 outliers final: 38 residues processed: 432 average time/residue: 1.5711 time to fit residues: 780.3595 Evaluate side-chains 443 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 391 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 363 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 L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 46 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 252 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 62 GLN G 101 ASN H 50 GLN ** M 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 558 GLN O 153 GLN P 51 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.083680 restraints weight = 39376.769| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.75 r_work: 0.2837 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29260 Z= 0.214 Angle : 0.523 15.045 39631 Z= 0.264 Chirality : 0.043 0.268 4278 Planarity : 0.004 0.062 5097 Dihedral : 8.716 179.900 4157 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 1.88 % Allowed : 16.26 % Favored : 81.87 % 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: 0.35 (0.14), residues: 3502 helix: 1.20 (0.15), residues: 1341 sheet: 0.24 (0.26), residues: 413 loop : -0.49 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.004 0.001 HIS Q 381 PHE 0.017 0.001 PHE G 126 TYR 0.017 0.001 TYR P 64 ARG 0.013 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11571.86 seconds wall clock time: 205 minutes 6.23 seconds (12306.23 seconds total)