Starting phenix.real_space_refine on Tue Feb 20 14:14:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu0_32807/02_2024/7wu0_32807.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu0_32807/02_2024/7wu0_32807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu0_32807/02_2024/7wu0_32807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu0_32807/02_2024/7wu0_32807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu0_32807/02_2024/7wu0_32807.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu0_32807/02_2024/7wu0_32807.pdb" } resolution = 3.3 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= 0.011 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1623 5.49 5 S 246 5.16 5 C 49127 2.51 5 N 15980 2.21 5 O 20678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 440": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 87656 Number of models: 1 Model: "" Number of chains: 37 Chain: "2" Number of atoms: 34680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1624, 34680 Inner-chain residues flagged as termini: ['pdbres=" C 21698 "'] Classifications: {'RNA': 1624} Modifications used: {'5*END': 1, 'rna2p_pur': 127, 'rna2p_pyr': 103, 'rna3p_pur': 736, 'rna3p_pyr': 658} Link IDs: {'rna2p': 229, 'rna3p': 1394} Chain breaks: 14 Chain: "F" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "P" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 984 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "Q" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "R" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1083 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "c" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 471 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 596 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1690 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1009 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "V" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "e" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 438 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "x" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1391 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 170} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "y" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2568 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 5062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5062 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 586} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "w" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2027 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 13, 'TRANS': 235} Chain: "t" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1066 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 7047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 7047 Classifications: {'peptide': 909} Link IDs: {'CIS': 1, 'PTRANS': 40, 'TRANS': 867} Chain breaks: 4 Chain: "v" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2589 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 311} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "y" 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 68748 SG CYS y 270 109.099 167.070 152.109 1.00 23.29 S ATOM 68768 SG CYS y 273 111.494 167.406 153.501 1.00 21.56 S ATOM 68865 SG CYS y 285 112.295 167.064 149.228 1.00 24.61 S ATOM 68887 SG CYS y 288 111.741 164.170 151.142 1.00 19.19 S Time building chain proxies: 33.54, per 1000 atoms: 0.38 Number of scatterers: 87656 At special positions: 0 Unit cell: (234.039, 249.924, 202.269, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 246 16.00 P 1623 15.00 O 20678 8.00 N 15980 7.00 C 49127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=0, symmetry=0 Time building additional restraints: 32.64 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN y 500 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 273 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 270 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 288 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 285 " Number of angles added : 6 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12488 Finding SS restraints... Secondary structure from input PDB file: 245 helices and 52 sheets defined 45.4% alpha, 14.1% beta 525 base pairs and 895 stacking pairs defined. Time for finding SS restraints: 25.96 Creating SS restraints... Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.805A pdb=" N MET F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 86 through 105 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 142 through 162 Processing helix chain 'F' and resid 168 through 182 Processing helix chain 'F' and resid 187 through 204 removed outlier: 3.809A pdb=" N ARG F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 29 removed outlier: 4.803A pdb=" N GLN M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 41 Processing helix chain 'M' and resid 58 through 72 removed outlier: 3.839A pdb=" N VAL M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 90 removed outlier: 3.521A pdb=" N LEU M 85 " --> pdb=" O ASP M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 132 Processing helix chain 'P' and resid 21 through 28 Processing helix chain 'P' and resid 31 through 35 removed outlier: 3.955A pdb=" N GLN P 35 " --> pdb=" O GLN P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 50 through 66 Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.709A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 120 removed outlier: 3.898A pdb=" N GLU P 118 " --> pdb=" O TYR P 115 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER P 120 " --> pdb=" O GLY P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Q' and resid 47 through 59 removed outlier: 4.247A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Proline residue: Q 54 - end of helix Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.579A pdb=" N ALA Q 64 " --> pdb=" O GLU Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 77 through 99 Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.737A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 Processing helix chain 'R' and resid 6 through 21 removed outlier: 3.691A pdb=" N TYR R 21 " --> pdb=" O ILE R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 39 removed outlier: 3.607A pdb=" N ALA R 39 " --> pdb=" O CYS R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 62 removed outlier: 3.616A pdb=" N GLN R 62 " --> pdb=" O MET R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 83 Processing helix chain 'R' and resid 99 through 109 Processing helix chain 'S' and resid 25 through 32 Processing helix chain 'S' and resid 37 through 48 Processing helix chain 'S' and resid 60 through 73 removed outlier: 3.590A pdb=" N ASN S 73 " --> pdb=" O THR S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 118 Processing helix chain 'S' and resid 119 through 128 Processing helix chain 'T' and resid 10 through 26 Processing helix chain 'T' and resid 51 through 67 removed outlier: 4.315A pdb=" N THR T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 79 Processing helix chain 'T' and resid 96 through 109 removed outlier: 3.560A pdb=" N ALA T 100 " --> pdb=" O SER T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 144 Processing helix chain 'Z' and resid 51 through 60 Processing helix chain 'Z' and resid 69 through 77 removed outlier: 3.553A pdb=" N VAL Z 73 " --> pdb=" O THR Z 69 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU Z 77 " --> pdb=" O VAL Z 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 94 Processing helix chain 'f' and resid 100 through 104 removed outlier: 3.777A pdb=" N LEU f 103 " --> pdb=" O LEU f 100 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS f 104 " --> pdb=" O ALA f 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 100 through 104' Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.537A pdb=" N GLU A 35 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN A 36 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.812A pdb=" N GLN A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.710A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.646A pdb=" N PHE A 203 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'B' and resid 57 through 62 removed outlier: 3.848A pdb=" N LEU B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 157 through 178 removed outlier: 3.936A pdb=" N THR B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 77 through 84 removed outlier: 4.182A pdb=" N ILE C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 4.309A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 160 Processing helix chain 'C' and resid 207 through 217 Processing helix chain 'C' and resid 232 through 250 removed outlier: 3.680A pdb=" N PHE C 236 " --> pdb=" O THR C 232 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.818A pdb=" N TRP C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 275 removed outlier: 4.141A pdb=" N LYS C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 4.059A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 57 through 66 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 262 Processing helix chain 'G' and resid 20 through 28 removed outlier: 3.696A pdb=" N LEU G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 181 through 230 Processing helix chain 'H' and resid 17 through 34 Processing helix chain 'H' and resid 37 through 43 Processing helix chain 'H' and resid 65 through 75 removed outlier: 4.109A pdb=" N LYS H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N SER H 71 " --> pdb=" O PRO H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 87 Processing helix chain 'H' and resid 117 through 120 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.957A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 180 Processing helix chain 'I' and resid 88 through 93 removed outlier: 3.727A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 130 through 138 Processing helix chain 'I' and resid 142 through 156 removed outlier: 3.813A pdb=" N ASN I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 191 through 206 Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 62 removed outlier: 4.189A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR J 62 " --> pdb=" O ARG J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 Processing helix chain 'J' and resid 93 through 100 removed outlier: 3.592A pdb=" N ILE J 97 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU J 98 " --> pdb=" O ASP J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.692A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 150 through 155 removed outlier: 4.437A pdb=" N LYS J 155 " --> pdb=" O LEU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 179 Processing helix chain 'L' and resid 23 through 30 removed outlier: 3.535A pdb=" N LYS L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 53 removed outlier: 3.501A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'O' and resid 70 through 89 Processing helix chain 'O' and resid 109 through 122 removed outlier: 3.538A pdb=" N GLN O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 62 Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 21 removed outlier: 3.687A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.526A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 94 Processing helix chain 'W' and resid 112 through 120 Processing helix chain 'X' and resid 9 through 22 Processing helix chain 'X' and resid 24 through 32 Processing helix chain 'X' and resid 34 through 39 Processing helix chain 'X' and resid 89 through 93 removed outlier: 3.557A pdb=" N ASN X 92 " --> pdb=" O GLY X 89 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 48 Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 93 Processing helix chain 'Y' and resid 103 through 116 removed outlier: 3.856A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 124 removed outlier: 4.308A pdb=" N ALA Y 121 " --> pdb=" O ARG Y 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 30 through 42 removed outlier: 3.543A pdb=" N ARG e 40 " --> pdb=" O MET e 36 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG e 41 " --> pdb=" O GLN e 37 " (cutoff:3.500A) Processing helix chain 'x' and resid 84 through 91 Processing helix chain 'x' and resid 91 through 102 Proline residue: x 98 - end of helix Processing helix chain 'x' and resid 128 through 143 removed outlier: 3.511A pdb=" N GLY x 143 " --> pdb=" O ALA x 139 " (cutoff:3.500A) Processing helix chain 'x' and resid 145 through 155 removed outlier: 3.885A pdb=" N LEU x 152 " --> pdb=" O ASP x 148 " (cutoff:3.500A) Processing helix chain 'x' and resid 173 through 185 Processing helix chain 'x' and resid 188 through 198 Processing helix chain 'x' and resid 214 through 229 Processing helix chain 'x' and resid 233 through 248 Processing helix chain 'y' and resid 10 through 16 removed outlier: 3.722A pdb=" N PHE y 14 " --> pdb=" O ASP y 10 " (cutoff:3.500A) Processing helix chain 'y' and resid 30 through 34 removed outlier: 3.545A pdb=" N VAL y 33 " --> pdb=" O ILE y 30 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 47 removed outlier: 3.554A pdb=" N ARG y 43 " --> pdb=" O ASP y 39 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA y 47 " --> pdb=" O ARG y 43 " (cutoff:3.500A) Processing helix chain 'y' and resid 59 through 71 Processing helix chain 'y' and resid 80 through 98 Processing helix chain 'y' and resid 99 through 103 removed outlier: 4.068A pdb=" N HIS y 102 " --> pdb=" O GLY y 99 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU y 103 " --> pdb=" O VAL y 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 99 through 103' Processing helix chain 'y' and resid 238 through 249 Processing helix chain 'y' and resid 380 through 385 removed outlier: 3.535A pdb=" N THR y 384 " --> pdb=" O SER y 380 " (cutoff:3.500A) Processing helix chain 'y' and resid 394 through 399 removed outlier: 3.587A pdb=" N ARG y 398 " --> pdb=" O ALA y 394 " (cutoff:3.500A) Processing helix chain 'u' and resid 49 through 73 Processing helix chain 'u' and resid 95 through 105 removed outlier: 3.645A pdb=" N ALA u 99 " --> pdb=" O SER u 95 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP u 105 " --> pdb=" O GLN u 101 " (cutoff:3.500A) Processing helix chain 'u' and resid 142 through 150 Processing helix chain 'u' and resid 167 through 181 Processing helix chain 'u' and resid 196 through 212 removed outlier: 3.841A pdb=" N ASP u 202 " --> pdb=" O LYS u 198 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU u 212 " --> pdb=" O SER u 208 " (cutoff:3.500A) Processing helix chain 'u' and resid 225 through 238 Processing helix chain 'u' and resid 244 through 250 removed outlier: 3.720A pdb=" N ARG u 250 " --> pdb=" O PHE u 246 " (cutoff:3.500A) Processing helix chain 'u' and resid 398 through 403 Processing helix chain 'u' and resid 465 through 483 Processing helix chain 'u' and resid 495 through 500 Processing helix chain 'u' and resid 523 through 526 Processing helix chain 'u' and resid 532 through 546 Processing helix chain 'u' and resid 567 through 574 Processing helix chain 'u' and resid 720 through 726 removed outlier: 3.557A pdb=" N LEU u 724 " --> pdb=" O ARG u 720 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 193 removed outlier: 4.005A pdb=" N VAL w 184 " --> pdb=" O ARG w 180 " (cutoff:3.500A) Processing helix chain 'w' and resid 212 through 220 Processing helix chain 'w' and resid 221 through 225 Processing helix chain 'w' and resid 226 through 240 Processing helix chain 'w' and resid 242 through 253 Processing helix chain 'w' and resid 253 through 266 Processing helix chain 'w' and resid 269 through 280 Processing helix chain 'w' and resid 282 through 290 removed outlier: 3.611A pdb=" N LYS w 288 " --> pdb=" O GLY w 284 " (cutoff:3.500A) Processing helix chain 'w' and resid 290 through 298 removed outlier: 3.930A pdb=" N GLY w 298 " --> pdb=" O LEU w 294 " (cutoff:3.500A) Processing helix chain 'w' and resid 301 through 315 Processing helix chain 'w' and resid 318 through 332 Processing helix chain 'w' and resid 335 through 347 removed outlier: 3.734A pdb=" N SER w 339 " --> pdb=" O SER w 335 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE w 340 " --> pdb=" O GLY w 336 " (cutoff:3.500A) Processing helix chain 'w' and resid 353 through 367 Processing helix chain 'w' and resid 375 through 389 removed outlier: 3.730A pdb=" N HIS w 379 " --> pdb=" O PRO w 375 " (cutoff:3.500A) Processing helix chain 'w' and resid 394 through 408 Processing helix chain 'w' and resid 412 through 423 removed outlier: 4.045A pdb=" N GLU w 416 " --> pdb=" O GLN w 412 " (cutoff:3.500A) Processing helix chain 't' and resid 292 through 307 Processing helix chain 't' and resid 426 through 469 Processing helix chain 'K' and resid 108 through 115 removed outlier: 3.549A pdb=" N GLU K 115 " --> pdb=" O GLN K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 122 removed outlier: 3.950A pdb=" N LYS K 122 " --> pdb=" O SER K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 141 removed outlier: 3.540A pdb=" N GLY K 140 " --> pdb=" O SER K 137 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS K 141 " --> pdb=" O GLN K 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 137 through 141' Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'K' and resid 151 through 156 Processing helix chain 'K' and resid 163 through 175 Processing helix chain 'K' and resid 179 through 205 removed outlier: 5.416A pdb=" N SER K 188 " --> pdb=" O ILE K 184 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASP K 189 " --> pdb=" O LYS K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 224 Processing helix chain 'K' and resid 233 through 243 Processing helix chain 'K' and resid 249 through 265 Processing helix chain 'K' and resid 280 through 295 removed outlier: 3.508A pdb=" N SER K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 315 removed outlier: 3.913A pdb=" N HIS K 306 " --> pdb=" O THR K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 335 Processing helix chain 'K' and resid 338 through 355 removed outlier: 3.556A pdb=" N ALA K 355 " --> pdb=" O SER K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 374 Processing helix chain 'K' and resid 375 through 377 No H-bonds generated for 'chain 'K' and resid 375 through 377' Processing helix chain 'K' and resid 385 through 405 removed outlier: 4.533A pdb=" N ALA K 389 " --> pdb=" O GLN K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 424 Proline residue: K 414 - end of helix Processing helix chain 'K' and resid 428 through 446 removed outlier: 3.619A pdb=" N LEU K 432 " --> pdb=" O HIS K 428 " (cutoff:3.500A) Processing helix chain 'K' and resid 447 through 449 No H-bonds generated for 'chain 'K' and resid 447 through 449' Processing helix chain 'K' and resid 450 through 455 removed outlier: 3.569A pdb=" N ILE K 454 " --> pdb=" O HIS K 450 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY K 455 " --> pdb=" O MET K 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 450 through 455' Processing helix chain 'K' and resid 463 through 478 removed outlier: 3.660A pdb=" N SER K 467 " --> pdb=" O GLY K 463 " (cutoff:3.500A) Processing helix chain 'K' and resid 486 through 506 removed outlier: 6.504A pdb=" N ARG K 503 " --> pdb=" O GLU K 499 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN K 504 " --> pdb=" O ALA K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 520 Processing helix chain 'K' and resid 527 through 542 Processing helix chain 'K' and resid 543 through 551 removed outlier: 3.591A pdb=" N VAL K 547 " --> pdb=" O GLY K 543 " (cutoff:3.500A) Processing helix chain 'K' and resid 568 through 577 Processing helix chain 'K' and resid 581 through 605 removed outlier: 3.861A pdb=" N PHE K 585 " --> pdb=" O ARG K 581 " (cutoff:3.500A) Proline residue: K 591 - end of helix Processing helix chain 'K' and resid 609 through 623 removed outlier: 3.724A pdb=" N LYS K 613 " --> pdb=" O THR K 609 " (cutoff:3.500A) Processing helix chain 'K' and resid 625 through 630 Processing helix chain 'K' and resid 635 through 640 removed outlier: 3.583A pdb=" N PHE K 640 " --> pdb=" O VAL K 636 " (cutoff:3.500A) Processing helix chain 'K' and resid 643 through 654 Processing helix chain 'K' and resid 657 through 671 Processing helix chain 'K' and resid 675 through 698 removed outlier: 3.854A pdb=" N ARG K 679 " --> pdb=" O ALA K 675 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASN K 688 " --> pdb=" O ARG K 684 " (cutoff:3.500A) Proline residue: K 691 - end of helix Processing helix chain 'K' and resid 709 through 723 removed outlier: 3.643A pdb=" N VAL K 713 " --> pdb=" O PRO K 709 " (cutoff:3.500A) Processing helix chain 'K' and resid 725 through 742 removed outlier: 3.596A pdb=" N VAL K 729 " --> pdb=" O ASP K 725 " (cutoff:3.500A) Processing helix chain 'K' and resid 746 through 761 Processing helix chain 'K' and resid 765 through 777 Processing helix chain 'K' and resid 778 through 782 removed outlier: 3.683A pdb=" N GLU K 781 " --> pdb=" O PRO K 778 " (cutoff:3.500A) Processing helix chain 'K' and resid 784 through 799 Processing helix chain 'K' and resid 804 through 813 Processing helix chain 'K' and resid 813 through 824 Processing helix chain 'K' and resid 832 through 843 removed outlier: 4.040A pdb=" N LYS K 838 " --> pdb=" O ARG K 834 " (cutoff:3.500A) Processing helix chain 'K' and resid 851 through 867 removed outlier: 3.655A pdb=" N ILE K 855 " --> pdb=" O HIS K 851 " (cutoff:3.500A) Proline residue: K 860 - end of helix Processing helix chain 'K' and resid 870 through 888 Processing helix chain 'K' and resid 894 through 905 Processing helix chain 'K' and resid 906 through 911 Processing helix chain 'K' and resid 913 through 929 removed outlier: 3.614A pdb=" N PHE K 929 " --> pdb=" O THR K 925 " (cutoff:3.500A) Processing helix chain 'K' and resid 936 through 951 Processing helix chain 'K' and resid 955 through 973 Processing helix chain 'K' and resid 974 through 991 removed outlier: 3.908A pdb=" N LYS K 980 " --> pdb=" O ALA K 976 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS K 981 " --> pdb=" O HIS K 977 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLN K 983 " --> pdb=" O ALA K 979 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU K 984 " --> pdb=" O LYS K 980 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL K 985 " --> pdb=" O HIS K 981 " (cutoff:3.500A) Processing helix chain 'K' and resid 994 through 1000 Processing helix chain 'K' and resid 1000 through 1015 Processing helix chain 'K' and resid 1016 through 1024 removed outlier: 3.859A pdb=" N VAL K1020 " --> pdb=" O GLY K1016 " (cutoff:3.500A) Processing helix chain 'K' and resid 1027 through 1042 removed outlier: 3.972A pdb=" N VAL K1031 " --> pdb=" O GLU K1027 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE K1035 " --> pdb=" O VAL K1031 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG K1036 " --> pdb=" O LEU K1032 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS K1037 " --> pdb=" O VAL K1033 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA K1038 " --> pdb=" O ASN K1034 " (cutoff:3.500A) Processing helix chain 'v' and resid 15 through 28 Processing helix chain 'v' and resid 34 through 42 removed outlier: 3.647A pdb=" N ILE v 38 " --> pdb=" O PRO v 34 " (cutoff:3.500A) Processing helix chain 'v' and resid 48 through 57 Processing helix chain 'v' and resid 76 through 91 Processing helix chain 'v' and resid 146 through 171 removed outlier: 4.116A pdb=" N TRP v 150 " --> pdb=" O HIS v 146 " (cutoff:3.500A) Processing helix chain 'v' and resid 197 through 199 No H-bonds generated for 'chain 'v' and resid 197 through 199' Processing helix chain 'v' and resid 204 through 222 removed outlier: 3.809A pdb=" N VAL v 208 " --> pdb=" O ASP v 204 " (cutoff:3.500A) Processing helix chain 'v' and resid 257 through 276 Processing helix chain 'v' and resid 497 through 522 Processing helix chain 'v' and resid 527 through 544 Processing sheet with id=AA1, first strand: chain 'F' and resid 123 through 127 removed outlier: 18.741A pdb=" N ILE c 43 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 12.525A pdb=" N ALA F 138 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN c 45 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS c 27 " --> pdb=" O ARG c 20 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG c 20 " --> pdb=" O CYS c 27 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN c 29 " --> pdb=" O LEU c 18 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS c 16 " --> pdb=" O ARG c 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 31 through 34 Processing sheet with id=AA3, first strand: chain 'P' and resid 76 through 78 removed outlier: 6.180A pdb=" N VAL P 76 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR P 97 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR P 78 " --> pdb=" O TYR P 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 9 through 16 Processing sheet with id=AA5, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'S' and resid 12 through 15 Processing sheet with id=AA7, first strand: chain 'T' and resid 81 through 83 Processing sheet with id=AA8, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AA9, first strand: chain 'Z' and resid 67 through 68 removed outlier: 6.673A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 10 through 11 Processing sheet with id=AB2, first strand: chain 'f' and resid 106 through 108 Processing sheet with id=AB3, first strand: chain 'f' and resid 133 through 134 Processing sheet with id=AB4, first strand: chain 'A' and resid 38 through 41 removed outlier: 7.049A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.778A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 50 removed outlier: 3.630A pdb=" N THR B 98 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B 91 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 50 removed outlier: 3.630A pdb=" N THR B 98 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 13.266A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 12.889A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ARG B 213 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N PHE B 211 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE B 142 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG B 213 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL B 140 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N MET B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG B 136 " --> pdb=" O MET B 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 102 through 116 removed outlier: 5.547A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 137 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AC1, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.601A pdb=" N ASN E 98 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.113A pdb=" N ILE E 136 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL E 131 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 217 through 221 removed outlier: 7.271A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.526A pdb=" N LEU G 106 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP G 57 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN G 110 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR G 48 " --> pdb=" O ALA G 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AC7, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC8, first strand: chain 'H' and resid 47 through 53 removed outlier: 3.839A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 185 through 188 removed outlier: 7.900A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.320A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.548A pdb=" N LYS I 37 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 62 through 67 removed outlier: 7.023A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE I 101 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS I 100 " --> pdb=" O ILE I 175 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AD5, first strand: chain 'L' and resid 72 through 82 removed outlier: 16.638A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.698A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS L 81 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 52 through 55 removed outlier: 6.054A pdb=" N GLY O 29 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LYS O 96 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS O 31 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG O 98 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE O 33 " --> pdb=" O ARG O 98 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU O 93 " --> pdb=" O ILE O 126 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ARG O 128 " --> pdb=" O LEU O 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 32 through 39 removed outlier: 4.953A pdb=" N GLN V 49 " --> pdb=" O GLU V 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AD9, first strand: chain 'W' and resid 80 through 81 Processing sheet with id=AE1, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.452A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Y' and resid 6 through 15 removed outlier: 3.865A pdb=" N VAL Y 24 " --> pdb=" O ARG Y 10 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG Y 20 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AE4, first strand: chain 'b' and resid 64 through 65 Processing sheet with id=AE5, first strand: chain 'x' and resid 75 through 79 removed outlier: 8.474A pdb=" N HIS y 129 " --> pdb=" O ILE x 107 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE x 109 " --> pdb=" O HIS y 129 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'x' and resid 159 through 164 Processing sheet with id=AE7, first strand: chain 'y' and resid 28 through 29 Processing sheet with id=AE8, first strand: chain 'y' and resid 111 through 112 removed outlier: 6.350A pdb=" N LYS y 111 " --> pdb=" O MET y 308 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'u' and resid 110 through 112 removed outlier: 9.574A pdb=" N LEU u 221 " --> pdb=" O TYR u 185 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU u 187 " --> pdb=" O LEU u 221 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'u' and resid 295 through 297 removed outlier: 6.941A pdb=" N ALA u 255 " --> pdb=" O TYR u 277 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N TYR u 277 " --> pdb=" O ALA u 255 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY u 270 " --> pdb=" O GLU u 564 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU u 564 " --> pdb=" O GLY u 270 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER u 563 " --> pdb=" O MET u 299 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N MET u 299 " --> pdb=" O SER u 563 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LYS u 300 " --> pdb=" O ALA u 347 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ALA u 347 " --> pdb=" O LYS u 300 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE u 302 " --> pdb=" O MET u 345 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL u 343 " --> pdb=" O ALA u 304 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'u' and resid 528 through 530 Processing sheet with id=AF3, first strand: chain 'u' and resid 622 through 625 removed outlier: 6.611A pdb=" N LYS u 669 " --> pdb=" O LEU u 678 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU u 678 " --> pdb=" O LYS u 669 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE u 629 " --> pdb=" O GLN u 641 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS u 639 " --> pdb=" O GLN u 631 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG u 696 " --> pdb=" O LEU u 640 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS u 752 " --> pdb=" O LYS u 742 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG u 714 " --> pdb=" O PRO u 703 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'v' and resid 62 through 66 Processing sheet with id=AF5, first strand: chain 'v' and resid 96 through 103 removed outlier: 5.842A pdb=" N GLN v 100 " --> pdb=" O ILE v 109 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE v 109 " --> pdb=" O GLN v 100 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY v 102 " --> pdb=" O SER v 107 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER v 107 " --> pdb=" O GLY v 102 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'v' and resid 194 through 195 Processing sheet with id=AF7, first strand: chain 'v' and resid 224 through 225 removed outlier: 4.039A pdb=" N ILE v 225 " --> pdb=" O VAL v 251 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL v 251 " --> pdb=" O ILE v 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 2482 hydrogen bonds defined for protein. 7152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1300 hydrogen bonds 2016 hydrogen bond angles 0 basepair planarities 525 basepair parallelities 895 stacking parallelities Total time for adding SS restraints: 66.67 Time building geometry restraints manager: 35.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10984 1.32 - 1.45: 33598 1.45 - 1.57: 44496 1.57 - 1.70: 3232 1.70 - 1.82: 384 Bond restraints: 92694 Sorted by residual: bond pdb=" C TYR K 907 " pdb=" N PRO K 908 " ideal model delta sigma weight residual 1.336 1.378 -0.043 1.08e-02 8.57e+03 1.56e+01 bond pdb=" CA ASN w 212 " pdb=" CB ASN w 212 " ideal model delta sigma weight residual 1.524 1.567 -0.043 1.30e-02 5.92e+03 1.09e+01 bond pdb=" N VAL K 378 " pdb=" CA VAL K 378 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N VAL T 30 " pdb=" CA VAL T 30 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.71e+00 bond pdb=" C GLY I 30 " pdb=" N ARG I 31 " ideal model delta sigma weight residual 1.331 1.289 0.042 1.59e-02 3.96e+03 7.09e+00 ... (remaining 92689 not shown) Histogram of bond angle deviations from ideal: 96.50 - 105.02: 8131 105.02 - 113.54: 55829 113.54 - 122.06: 50372 122.06 - 130.58: 17803 130.58 - 139.10: 780 Bond angle restraints: 132915 Sorted by residual: angle pdb=" C GLN F 65 " pdb=" N CYS F 66 " pdb=" CA CYS F 66 " ideal model delta sigma weight residual 120.39 129.61 -9.22 1.39e+00 5.18e-01 4.40e+01 angle pdb=" N GLY F 80 " pdb=" CA GLY F 80 " pdb=" C GLY F 80 " ideal model delta sigma weight residual 112.50 119.54 -7.04 1.16e+00 7.43e-01 3.69e+01 angle pdb=" C LEU R 109 " pdb=" N ASP R 110 " pdb=" CA ASP R 110 " ideal model delta sigma weight residual 125.66 135.82 -10.16 1.85e+00 2.92e-01 3.02e+01 angle pdb=" N THR M 16 " pdb=" CA THR M 16 " pdb=" C THR M 16 " ideal model delta sigma weight residual 114.04 107.45 6.59 1.24e+00 6.50e-01 2.82e+01 angle pdb=" CA PRO P 109 " pdb=" N PRO P 109 " pdb=" CD PRO P 109 " ideal model delta sigma weight residual 112.00 104.70 7.30 1.40e+00 5.10e-01 2.72e+01 ... (remaining 132910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 53710 35.78 - 71.56: 4394 71.56 - 107.34: 539 107.34 - 143.12: 18 143.12 - 178.89: 25 Dihedral angle restraints: 58686 sinusoidal: 39420 harmonic: 19266 Sorted by residual: dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual 200.00 22.77 177.23 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 823 " pdb=" C1' U 2 823 " pdb=" N1 U 2 823 " pdb=" C2 U 2 823 " ideal model delta sinusoidal sigma weight residual 200.00 24.45 175.55 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C 2 853 " pdb=" C1' C 2 853 " pdb=" N1 C 2 853 " pdb=" C2 C 2 853 " ideal model delta sinusoidal sigma weight residual -160.00 15.08 -175.08 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 58683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 15306 0.090 - 0.179: 867 0.179 - 0.269: 64 0.269 - 0.358: 17 0.358 - 0.448: 2 Chirality restraints: 16256 Sorted by residual: chirality pdb=" CB VAL A 140 " pdb=" CA VAL A 140 " pdb=" CG1 VAL A 140 " pdb=" CG2 VAL A 140 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CB ILE v 32 " pdb=" CA ILE v 32 " pdb=" CG1 ILE v 32 " pdb=" CG2 ILE v 32 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB VAL K 378 " pdb=" CA VAL K 378 " pdb=" CG1 VAL K 378 " pdb=" CG2 VAL K 378 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 16253 not shown) Planarity restraints: 10833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL v 175 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO v 176 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO v 176 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO v 176 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C 2 492 " -0.006 2.00e-02 2.50e+03 2.63e-02 1.56e+01 pdb=" N1 C 2 492 " 0.001 2.00e-02 2.50e+03 pdb=" C2 C 2 492 " -0.061 2.00e-02 2.50e+03 pdb=" O2 C 2 492 " 0.045 2.00e-02 2.50e+03 pdb=" N3 C 2 492 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C 2 492 " -0.010 2.00e-02 2.50e+03 pdb=" N4 C 2 492 " 0.005 2.00e-02 2.50e+03 pdb=" C5 C 2 492 " 0.012 2.00e-02 2.50e+03 pdb=" C6 C 2 492 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 509 " -0.021 2.00e-02 2.50e+03 2.18e-02 1.43e+01 pdb=" N9 G 2 509 " 0.006 2.00e-02 2.50e+03 pdb=" C8 G 2 509 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G 2 509 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G 2 509 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G 2 509 " 0.037 2.00e-02 2.50e+03 pdb=" O6 G 2 509 " -0.034 2.00e-02 2.50e+03 pdb=" N1 G 2 509 " -0.018 2.00e-02 2.50e+03 pdb=" C2 G 2 509 " 0.044 2.00e-02 2.50e+03 pdb=" N2 G 2 509 " -0.022 2.00e-02 2.50e+03 pdb=" N3 G 2 509 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G 2 509 " 0.000 2.00e-02 2.50e+03 ... (remaining 10830 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 7296 2.74 - 3.28: 78086 3.28 - 3.82: 163523 3.82 - 4.36: 197436 4.36 - 4.90: 293713 Nonbonded interactions: 740054 Sorted by model distance: nonbonded pdb=" O2' G 21528 " pdb=" OP1 C 21666 " model vdw 2.194 2.440 nonbonded pdb=" O2' A 21291 " pdb=" OH TYR f 140 " model vdw 2.229 2.440 nonbonded pdb=" O6 G 21722 " pdb=" O2 U 21812 " model vdw 2.230 2.432 nonbonded pdb=" OG1 THR B 129 " pdb=" O ASN B 179 " model vdw 2.240 2.440 nonbonded pdb=" O GLY K 936 " pdb=" OG1 THR K 939 " model vdw 2.243 2.440 ... (remaining 740049 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: 2.600 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: 0.080 Extract box with map and model: 12.530 Check model and map are aligned: 0.960 Set scattering table: 0.630 Process input model: 240.760 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 262.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 : 0.003 0.097 92694 Z= 0.217 Angle : 0.813 15.492 132915 Z= 0.428 Chirality : 0.044 0.448 16256 Planarity : 0.006 0.100 10833 Dihedral : 21.592 178.894 46198 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 0.05 % Allowed : 0.44 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.03 % 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: -1.24 (0.09), residues: 6547 helix: -0.22 (0.09), residues: 2765 sheet: -0.41 (0.17), residues: 857 loop : -1.48 (0.10), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 390 HIS 0.014 0.001 HIS F 101 PHE 0.060 0.002 PHE t 263 TYR 0.029 0.002 TYR G 28 ARG 0.017 0.001 ARG t 428 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 702 time to evaluate : 5.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 248 TYR cc_start: 0.6365 (t80) cc_final: 0.6093 (t80) REVERT: G 91 GLU cc_start: 0.7299 (pp20) cc_final: 0.6195 (mm-30) REVERT: x 156 ASP cc_start: 0.7871 (m-30) cc_final: 0.7570 (m-30) outliers start: 3 outliers final: 1 residues processed: 705 average time/residue: 0.7948 time to fit residues: 965.5844 Evaluate side-chains 537 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 536 time to evaluate : 5.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 121 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 685 optimal weight: 4.9990 chunk 615 optimal weight: 7.9990 chunk 341 optimal weight: 0.9990 chunk 210 optimal weight: 30.0000 chunk 415 optimal weight: 0.2980 chunk 328 optimal weight: 0.9990 chunk 636 optimal weight: 0.9990 chunk 246 optimal weight: 20.0000 chunk 386 optimal weight: 30.0000 chunk 473 optimal weight: 0.5980 chunk 737 optimal weight: 7.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN F 107 ASN F 110 GLN P 24 GLN P 54 HIS Q 48 GLN R 121 GLN S 87 GLN S 97 GLN ** Z 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 GLN A 215 GLN B 208 HIS ** G 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 GLN V 82 ASN b 83 GLN x 196 ASN x 217 ASN u 301 GLN ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 HIS ** K 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 900 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 92694 Z= 0.137 Angle : 0.557 10.299 132915 Z= 0.287 Chirality : 0.036 0.249 16256 Planarity : 0.004 0.067 10833 Dihedral : 22.695 179.630 32659 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 1.01 % Allowed : 6.56 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.03 % 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: -0.37 (0.10), residues: 6547 helix: 0.86 (0.10), residues: 2806 sheet: -0.31 (0.17), residues: 866 loop : -1.33 (0.11), residues: 2875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 623 HIS 0.007 0.001 HIS G 70 PHE 0.020 0.001 PHE w 362 TYR 0.020 0.001 TYR t 301 ARG 0.008 0.000 ARG J 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 579 time to evaluate : 5.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 125 PRO cc_start: 0.7350 (Cg_exo) cc_final: 0.7135 (Cg_endo) REVERT: B 103 MET cc_start: 0.8134 (tmm) cc_final: 0.7364 (ttt) REVERT: C 248 TYR cc_start: 0.6380 (t80) cc_final: 0.6172 (t80) REVERT: G 91 GLU cc_start: 0.7304 (pp20) cc_final: 0.6296 (mm-30) REVERT: I 170 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7513 (mtmm) REVERT: b 83 GLN cc_start: 0.6581 (OUTLIER) cc_final: 0.6005 (pp30) REVERT: x 156 ASP cc_start: 0.7841 (m-30) cc_final: 0.7609 (m-30) REVERT: v 101 MET cc_start: 0.4943 (mmp) cc_final: 0.4013 (mmp) outliers start: 58 outliers final: 34 residues processed: 605 average time/residue: 0.7839 time to fit residues: 823.8351 Evaluate side-chains 556 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 520 time to evaluate : 5.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 56 HIS Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 170 LYS Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 83 GLN Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain u residue 144 HIS Chi-restraints excluded: chain u residue 223 LEU Chi-restraints excluded: chain u residue 278 VAL Chi-restraints excluded: chain w residue 212 ASN Chi-restraints excluded: chain t residue 259 HIS Chi-restraints excluded: chain t residue 260 ASP Chi-restraints excluded: chain v residue 246 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 409 optimal weight: 0.6980 chunk 228 optimal weight: 0.9990 chunk 613 optimal weight: 1.9990 chunk 502 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 738 optimal weight: 50.0000 chunk 798 optimal weight: 8.9990 chunk 657 optimal weight: 30.0000 chunk 732 optimal weight: 40.0000 chunk 251 optimal weight: 40.0000 chunk 592 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 110 GLN P 24 GLN ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN R 121 GLN T 51 ASN A 36 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 HIS B 208 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 HIS ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 210 HIS y 102 HIS y 218 GLN ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 422 GLN ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 182 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 92694 Z= 0.208 Angle : 0.578 13.399 132915 Z= 0.294 Chirality : 0.037 0.281 16256 Planarity : 0.004 0.062 10833 Dihedral : 22.577 179.032 32656 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 1.47 % Allowed : 9.23 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.03 % 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: -0.06 (0.10), residues: 6547 helix: 1.22 (0.10), residues: 2812 sheet: -0.31 (0.17), residues: 873 loop : -1.23 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 390 HIS 0.007 0.001 HIS w 363 PHE 0.021 0.002 PHE t 263 TYR 0.034 0.002 TYR G 28 ARG 0.007 0.000 ARG c 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 561 time to evaluate : 5.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 125 PRO cc_start: 0.7534 (Cg_exo) cc_final: 0.7270 (Cg_endo) REVERT: A 79 SER cc_start: 0.8473 (p) cc_final: 0.8169 (t) REVERT: A 215 GLN cc_start: 0.7561 (tt0) cc_final: 0.7274 (tt0) REVERT: C 248 TYR cc_start: 0.6460 (t80) cc_final: 0.5801 (t80) REVERT: E 87 MET cc_start: 0.7858 (tpp) cc_final: 0.7597 (mpp) REVERT: G 32 MET cc_start: 0.7831 (tpp) cc_final: 0.7310 (ttm) REVERT: W 14 ILE cc_start: 0.8610 (pt) cc_final: 0.8172 (mt) REVERT: W 57 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.6880 (mmt180) REVERT: x 156 ASP cc_start: 0.7883 (m-30) cc_final: 0.7630 (m-30) REVERT: y 280 MET cc_start: 0.7942 (mmm) cc_final: 0.7547 (mmm) REVERT: u 123 MET cc_start: 0.7950 (tpp) cc_final: 0.7357 (tpt) REVERT: w 358 ASP cc_start: 0.6057 (m-30) cc_final: 0.5780 (m-30) outliers start: 84 outliers final: 62 residues processed: 607 average time/residue: 0.7931 time to fit residues: 833.1495 Evaluate side-chains 584 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 521 time to evaluate : 5.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 41 MET Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain c residue 54 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain u residue 96 LEU Chi-restraints excluded: chain u residue 144 HIS Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 223 LEU Chi-restraints excluded: chain u residue 278 VAL Chi-restraints excluded: chain u residue 359 VAL Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain w residue 212 ASN Chi-restraints excluded: chain w residue 315 CYS Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 260 ASP Chi-restraints excluded: chain t residue 426 ASP Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain v residue 244 MET Chi-restraints excluded: chain v residue 246 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 729 optimal weight: 50.0000 chunk 555 optimal weight: 5.9990 chunk 383 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 352 optimal weight: 7.9990 chunk 496 optimal weight: 4.9990 chunk 741 optimal weight: 20.0000 chunk 784 optimal weight: 2.9990 chunk 387 optimal weight: 6.9990 chunk 702 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 110 GLN ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN A 36 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN B 208 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN E 188 ASN H 44 ASN H 73 GLN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 HIS L 112 HIS O 32 HIS X 23 HIS ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN ** x 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 102 HIS u 74 GLN ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 397 GLN ** w 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 811 GLN ** v 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 92 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 92694 Z= 0.395 Angle : 0.721 11.260 132915 Z= 0.363 Chirality : 0.044 0.347 16256 Planarity : 0.006 0.075 10833 Dihedral : 22.735 179.940 32656 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 2.32 % Allowed : 11.63 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.10), residues: 6547 helix: 1.16 (0.10), residues: 2797 sheet: -0.53 (0.17), residues: 868 loop : -1.32 (0.11), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP w 213 HIS 0.012 0.001 HIS u 676 PHE 0.036 0.002 PHE X 105 TYR 0.028 0.002 TYR C 248 ARG 0.011 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 540 time to evaluate : 6.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8479 (p) cc_final: 0.8237 (t) REVERT: J 27 GLN cc_start: 0.7664 (mt0) cc_final: 0.7462 (mt0) REVERT: J 159 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7248 (t80) REVERT: L 91 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: O 75 MET cc_start: 0.7410 (tmm) cc_final: 0.7058 (ttm) REVERT: W 57 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.6427 (mmt-90) REVERT: Y 74 MET cc_start: 0.7760 (mtm) cc_final: 0.7519 (mtm) REVERT: x 156 ASP cc_start: 0.7934 (m-30) cc_final: 0.7700 (m-30) REVERT: y 280 MET cc_start: 0.8094 (mmm) cc_final: 0.7751 (mmm) REVERT: u 123 MET cc_start: 0.8005 (tpp) cc_final: 0.7554 (tpt) outliers start: 133 outliers final: 83 residues processed: 633 average time/residue: 0.8097 time to fit residues: 891.2130 Evaluate side-chains 587 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 501 time to evaluate : 5.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 41 MET Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 54 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 53 GLU Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain x residue 246 SER Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 160 LEU Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 223 LEU Chi-restraints excluded: chain u residue 278 VAL Chi-restraints excluded: chain u residue 359 VAL Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain w residue 212 ASN Chi-restraints excluded: chain w residue 312 ILE Chi-restraints excluded: chain w residue 315 CYS Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 260 ASP Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain v residue 64 TRP Chi-restraints excluded: chain v residue 112 VAL Chi-restraints excluded: chain v residue 244 MET Chi-restraints excluded: chain v residue 246 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 653 optimal weight: 6.9990 chunk 445 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 584 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 669 optimal weight: 4.9990 chunk 542 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 400 optimal weight: 0.8980 chunk 704 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 HIS F 110 GLN P 24 GLN ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN S 72 GLN A 36 GLN A 50 ASN B 208 HIS H 73 GLN N 5 HIS V 33 GLN X 61 GLN x 196 ASN y 102 HIS ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 290 HIS ** w 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 92694 Z= 0.209 Angle : 0.591 10.973 132915 Z= 0.300 Chirality : 0.038 0.293 16256 Planarity : 0.004 0.059 10833 Dihedral : 22.622 179.333 32656 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 2.13 % Allowed : 13.56 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.03 % 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: 0.03 (0.10), residues: 6547 helix: 1.42 (0.10), residues: 2814 sheet: -0.50 (0.17), residues: 863 loop : -1.24 (0.11), residues: 2870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP w 213 HIS 0.007 0.001 HIS O 43 PHE 0.028 0.001 PHE w 362 TYR 0.024 0.001 TYR F 188 ARG 0.005 0.000 ARG W 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 532 time to evaluate : 5.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 90 VAL cc_start: 0.7597 (m) cc_final: 0.7381 (m) REVERT: P 125 PRO cc_start: 0.7693 (Cg_exo) cc_final: 0.7449 (Cg_endo) REVERT: A 79 SER cc_start: 0.8491 (p) cc_final: 0.8266 (t) REVERT: E 171 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7371 (p0) REVERT: J 159 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7346 (t80) REVERT: L 33 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7181 (tt) REVERT: L 91 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: O 37 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.6593 (p90) REVERT: O 61 LYS cc_start: 0.7197 (mmtm) cc_final: 0.6957 (mptt) REVERT: O 75 MET cc_start: 0.7355 (tmm) cc_final: 0.6946 (ttm) REVERT: W 14 ILE cc_start: 0.8699 (pt) cc_final: 0.8313 (mt) REVERT: W 57 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.6649 (mmt180) REVERT: x 156 ASP cc_start: 0.7804 (m-30) cc_final: 0.7554 (m-30) REVERT: y 280 MET cc_start: 0.7986 (mmm) cc_final: 0.7612 (mmm) REVERT: u 123 MET cc_start: 0.8003 (tpp) cc_final: 0.7510 (tpt) REVERT: u 679 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7967 (pt) REVERT: u 766 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8562 (pp) REVERT: K 291 GLU cc_start: 0.5471 (OUTLIER) cc_final: 0.5251 (pp20) outliers start: 122 outliers final: 79 residues processed: 614 average time/residue: 0.8786 time to fit residues: 949.5979 Evaluate side-chains 598 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 510 time to evaluate : 5.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 41 MET Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain T residue 137 GLN Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 54 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain x residue 246 SER Chi-restraints excluded: chain y residue 25 LYS Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 96 LEU Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 223 LEU Chi-restraints excluded: chain u residue 278 VAL Chi-restraints excluded: chain u residue 359 VAL Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 260 ASP Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 291 GLU Chi-restraints excluded: chain v residue 122 LEU Chi-restraints excluded: chain v residue 244 MET Chi-restraints excluded: chain v residue 246 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 264 optimal weight: 30.0000 chunk 706 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 460 optimal weight: 0.9990 chunk 193 optimal weight: 20.0000 chunk 785 optimal weight: 10.0000 chunk 652 optimal weight: 4.9990 chunk 363 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 412 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 110 GLN P 24 GLN P 46 ASN ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN A 36 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS C 134 ASN ** y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 506 HIS v 59 HIS ** v 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 92694 Z= 0.345 Angle : 0.682 11.182 132915 Z= 0.344 Chirality : 0.042 0.330 16256 Planarity : 0.005 0.068 10833 Dihedral : 22.642 179.756 32656 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 2.50 % Allowed : 14.51 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.03 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.10), residues: 6547 helix: 1.36 (0.10), residues: 2816 sheet: -0.48 (0.17), residues: 837 loop : -1.29 (0.11), residues: 2894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 390 HIS 0.013 0.001 HIS u 144 PHE 0.035 0.002 PHE X 105 TYR 0.028 0.002 TYR G 28 ARG 0.013 0.001 ARG K 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 525 time to evaluate : 5.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8459 (p) cc_final: 0.8183 (t) REVERT: I 105 ASP cc_start: 0.8072 (t0) cc_final: 0.7629 (t0) REVERT: L 91 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: O 37 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.6863 (p90) REVERT: W 14 ILE cc_start: 0.8723 (pt) cc_final: 0.8279 (mt) REVERT: W 57 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.6458 (mmt-90) REVERT: x 122 LYS cc_start: 0.7061 (mmtt) cc_final: 0.6821 (mmtt) REVERT: x 156 ASP cc_start: 0.7816 (m-30) cc_final: 0.7563 (m-30) REVERT: y 280 MET cc_start: 0.8003 (mmm) cc_final: 0.7622 (mmm) REVERT: u 144 HIS cc_start: 0.6360 (m90) cc_final: 0.6040 (m-70) REVERT: u 679 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8037 (pt) REVERT: u 766 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8568 (pp) REVERT: K 394 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.5343 (pmm) outliers start: 143 outliers final: 111 residues processed: 632 average time/residue: 0.8021 time to fit residues: 883.6531 Evaluate side-chains 615 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 498 time to evaluate : 5.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 41 MET Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain S residue 71 MET Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 23 LYS Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 54 ASP Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain x residue 246 SER Chi-restraints excluded: chain y residue 25 LYS Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 130 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 160 LEU Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 223 LEU Chi-restraints excluded: chain u residue 278 VAL Chi-restraints excluded: chain u residue 283 LEU Chi-restraints excluded: chain u residue 359 VAL Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain w residue 312 ILE Chi-restraints excluded: chain w residue 315 CYS Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 260 ASP Chi-restraints excluded: chain t residue 426 ASP Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 394 MET Chi-restraints excluded: chain v residue 122 LEU Chi-restraints excluded: chain v residue 244 MET Chi-restraints excluded: chain v residue 246 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 757 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 447 optimal weight: 0.9980 chunk 573 optimal weight: 0.5980 chunk 444 optimal weight: 8.9990 chunk 661 optimal weight: 7.9990 chunk 438 optimal weight: 3.9990 chunk 782 optimal weight: 4.9990 chunk 489 optimal weight: 1.9990 chunk 477 optimal weight: 7.9990 chunk 361 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 110 GLN P 24 GLN ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN R 26 ASN R 121 GLN ** Z 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS C 134 ASN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN y 85 GLN ** w 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 92694 Z= 0.209 Angle : 0.599 17.210 132915 Z= 0.303 Chirality : 0.038 0.290 16256 Planarity : 0.004 0.062 10833 Dihedral : 22.566 179.183 32656 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 2.30 % Allowed : 15.17 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.03 % Twisted Proline : 0.35 % 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: 0.13 (0.10), residues: 6547 helix: 1.53 (0.10), residues: 2822 sheet: -0.51 (0.17), residues: 854 loop : -1.20 (0.11), residues: 2871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 390 HIS 0.007 0.001 HIS O 43 PHE 0.033 0.001 PHE w 362 TYR 0.035 0.002 TYR t 302 ARG 0.007 0.000 ARG W 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 539 time to evaluate : 5.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 125 PRO cc_start: 0.7756 (Cg_exo) cc_final: 0.7514 (Cg_endo) REVERT: A 79 SER cc_start: 0.8439 (p) cc_final: 0.8217 (t) REVERT: A 215 GLN cc_start: 0.7478 (tt0) cc_final: 0.7231 (tt0) REVERT: E 171 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7415 (p0) REVERT: G 91 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6563 (tt0) REVERT: I 105 ASP cc_start: 0.7999 (t0) cc_final: 0.7571 (t0) REVERT: J 159 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7424 (t80) REVERT: L 33 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7221 (tt) REVERT: L 91 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: O 37 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6594 (p90) REVERT: O 141 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6682 (ttt90) REVERT: V 1 MET cc_start: 0.7214 (tpp) cc_final: 0.6767 (tpp) REVERT: W 14 ILE cc_start: 0.8710 (pt) cc_final: 0.8298 (mt) REVERT: W 57 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.6538 (mmt180) REVERT: X 66 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8259 (mp) REVERT: b 65 GLN cc_start: 0.7545 (mm110) cc_final: 0.7184 (mm110) REVERT: x 156 ASP cc_start: 0.7787 (m-30) cc_final: 0.7529 (m-30) REVERT: y 280 MET cc_start: 0.7853 (mmm) cc_final: 0.7458 (mmm) REVERT: u 217 HIS cc_start: 0.7374 (OUTLIER) cc_final: 0.6499 (p90) REVERT: u 679 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.8004 (pt) REVERT: u 766 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8564 (pp) REVERT: K 394 MET cc_start: 0.5710 (OUTLIER) cc_final: 0.5385 (pmm) outliers start: 132 outliers final: 93 residues processed: 636 average time/residue: 0.8177 time to fit residues: 900.4750 Evaluate side-chains 615 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 509 time to evaluate : 5.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 41 MET Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 23 LYS Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain T residue 137 GLN Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 54 ASP Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 141 ARG Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain x residue 121 CYS Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain y residue 25 LYS Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 96 LEU Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 223 LEU Chi-restraints excluded: chain u residue 278 VAL Chi-restraints excluded: chain u residue 359 VAL Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain w residue 312 ILE Chi-restraints excluded: chain w residue 315 CYS Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 260 ASP Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 198 MET Chi-restraints excluded: chain K residue 394 MET Chi-restraints excluded: chain v residue 122 LEU Chi-restraints excluded: chain v residue 244 MET Chi-restraints excluded: chain v residue 246 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 484 optimal weight: 0.8980 chunk 312 optimal weight: 3.9990 chunk 467 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 153 optimal weight: 50.0000 chunk 151 optimal weight: 10.0000 chunk 497 optimal weight: 5.9990 chunk 533 optimal weight: 0.0970 chunk 386 optimal weight: 9.9990 chunk 72 optimal weight: 50.0000 chunk 615 optimal weight: 9.9990 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 110 GLN P 46 ASN ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN R 121 GLN A 36 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN O 38 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 92694 Z= 0.247 Angle : 0.622 16.323 132915 Z= 0.314 Chirality : 0.039 0.304 16256 Planarity : 0.005 0.062 10833 Dihedral : 22.528 179.196 32656 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 2.43 % Allowed : 15.50 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.03 % Twisted Proline : 0.35 % 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: 0.14 (0.10), residues: 6547 helix: 1.53 (0.10), residues: 2816 sheet: -0.55 (0.17), residues: 860 loop : -1.17 (0.11), residues: 2871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP w 213 HIS 0.006 0.001 HIS u 676 PHE 0.037 0.002 PHE t 263 TYR 0.033 0.002 TYR t 302 ARG 0.007 0.000 ARG W 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 523 time to evaluate : 5.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8464 (p) cc_final: 0.8238 (t) REVERT: B 133 TYR cc_start: 0.8629 (m-80) cc_final: 0.8362 (m-80) REVERT: G 91 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6605 (tt0) REVERT: I 105 ASP cc_start: 0.7985 (t0) cc_final: 0.7580 (t0) REVERT: J 159 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7447 (t80) REVERT: L 33 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7257 (tt) REVERT: L 49 GLU cc_start: 0.6288 (tp30) cc_final: 0.5932 (tp30) REVERT: L 91 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: O 37 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6668 (p90) REVERT: O 61 LYS cc_start: 0.7329 (mmtm) cc_final: 0.7082 (mptt) REVERT: O 141 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.6704 (ttt90) REVERT: V 1 MET cc_start: 0.7228 (tpp) cc_final: 0.6760 (tpp) REVERT: W 14 ILE cc_start: 0.8704 (pt) cc_final: 0.8260 (mt) REVERT: W 57 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.6523 (mmt-90) REVERT: X 66 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8297 (mp) REVERT: X 119 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7332 (mmt-90) REVERT: x 156 ASP cc_start: 0.7778 (m-30) cc_final: 0.7520 (m-30) REVERT: y 280 MET cc_start: 0.7817 (mmm) cc_final: 0.7416 (mmm) REVERT: u 217 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.6488 (p90) REVERT: u 679 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8030 (pt) REVERT: u 766 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8563 (pp) REVERT: K 394 MET cc_start: 0.5711 (OUTLIER) cc_final: 0.5432 (pmm) outliers start: 139 outliers final: 108 residues processed: 629 average time/residue: 0.8759 time to fit residues: 963.7517 Evaluate side-chains 625 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 504 time to evaluate : 5.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 41 MET Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 23 LYS Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain T residue 137 GLN Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 54 ASP Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 141 ARG Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain x residue 121 CYS Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain y residue 25 LYS Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 82 THR Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 51 VAL Chi-restraints excluded: chain u residue 96 LEU Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 223 LEU Chi-restraints excluded: chain u residue 278 VAL Chi-restraints excluded: chain u residue 283 LEU Chi-restraints excluded: chain u residue 359 VAL Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain w residue 312 ILE Chi-restraints excluded: chain w residue 315 CYS Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 260 ASP Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 394 MET Chi-restraints excluded: chain v residue 112 VAL Chi-restraints excluded: chain v residue 122 LEU Chi-restraints excluded: chain v residue 244 MET Chi-restraints excluded: chain v residue 246 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 711 optimal weight: 50.0000 chunk 749 optimal weight: 8.9990 chunk 684 optimal weight: 3.9990 chunk 729 optimal weight: 10.0000 chunk 438 optimal weight: 3.9990 chunk 317 optimal weight: 10.0000 chunk 572 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 659 optimal weight: 5.9990 chunk 689 optimal weight: 2.9990 chunk 726 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN F 110 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 24 GLN ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN R 121 GLN A 36 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 719 ASN ** v 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 118 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 92694 Z= 0.328 Angle : 0.681 17.229 132915 Z= 0.343 Chirality : 0.042 0.327 16256 Planarity : 0.005 0.080 10833 Dihedral : 22.579 179.707 32656 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 2.46 % Allowed : 15.80 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.03 % Twisted Proline : 0.35 % 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: 0.01 (0.10), residues: 6547 helix: 1.43 (0.10), residues: 2815 sheet: -0.59 (0.17), residues: 841 loop : -1.24 (0.11), residues: 2891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP v 260 HIS 0.008 0.001 HIS X 46 PHE 0.033 0.002 PHE X 105 TYR 0.030 0.002 TYR t 301 ARG 0.009 0.001 ARG K 415 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 519 time to evaluate : 5.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 12 MET cc_start: 0.2483 (ppp) cc_final: 0.2025 (ppp) REVERT: A 79 SER cc_start: 0.8484 (p) cc_final: 0.8189 (t) REVERT: G 91 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6799 (tt0) REVERT: I 105 ASP cc_start: 0.7997 (t0) cc_final: 0.7610 (t0) REVERT: I 155 ASN cc_start: 0.7982 (t0) cc_final: 0.7533 (t0) REVERT: J 27 GLN cc_start: 0.7638 (mt0) cc_final: 0.7424 (mt0) REVERT: J 159 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7503 (t80) REVERT: L 33 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7369 (tt) REVERT: L 91 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: O 37 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.6694 (p90) REVERT: O 61 LYS cc_start: 0.7350 (mmtm) cc_final: 0.7104 (mptt) REVERT: O 141 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.6796 (ttt90) REVERT: V 1 MET cc_start: 0.7296 (tpp) cc_final: 0.6825 (tpp) REVERT: W 14 ILE cc_start: 0.8757 (pt) cc_final: 0.8280 (mt) REVERT: W 57 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.6372 (mmt-90) REVERT: X 119 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7407 (mmt-90) REVERT: x 156 ASP cc_start: 0.7782 (m-30) cc_final: 0.7523 (m-30) REVERT: y 280 MET cc_start: 0.7827 (mmm) cc_final: 0.7434 (mmm) REVERT: u 217 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.6510 (p90) REVERT: u 679 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8064 (pt) REVERT: u 766 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8585 (pp) outliers start: 141 outliers final: 106 residues processed: 630 average time/residue: 0.7831 time to fit residues: 863.1166 Evaluate side-chains 622 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 505 time to evaluate : 5.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 41 MET Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain T residue 137 GLN Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 141 ARG Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 13 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain x residue 121 CYS Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain y residue 25 LYS Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 82 THR Chi-restraints excluded: chain y residue 130 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 51 VAL Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 160 LEU Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 223 LEU Chi-restraints excluded: chain u residue 278 VAL Chi-restraints excluded: chain u residue 283 LEU Chi-restraints excluded: chain u residue 359 VAL Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain w residue 212 ASN Chi-restraints excluded: chain w residue 315 CYS Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 260 ASP Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 466 GLN Chi-restraints excluded: chain v residue 64 TRP Chi-restraints excluded: chain v residue 112 VAL Chi-restraints excluded: chain v residue 122 LEU Chi-restraints excluded: chain v residue 244 MET Chi-restraints excluded: chain v residue 246 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 478 optimal weight: 3.9990 chunk 771 optimal weight: 40.0000 chunk 470 optimal weight: 5.9990 chunk 365 optimal weight: 0.0980 chunk 536 optimal weight: 0.8980 chunk 808 optimal weight: 6.9990 chunk 744 optimal weight: 0.1980 chunk 644 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 497 optimal weight: 5.9990 chunk 394 optimal weight: 6.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN R 121 GLN A 36 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN C 134 ASN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 632 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 92694 Z= 0.201 Angle : 0.610 15.325 132915 Z= 0.308 Chirality : 0.038 0.289 16256 Planarity : 0.004 0.062 10833 Dihedral : 22.530 179.990 32656 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.74 % Rotamer: Outliers : 1.97 % Allowed : 16.53 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.03 % Twisted Proline : 0.35 % 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: 0.14 (0.10), residues: 6547 helix: 1.56 (0.10), residues: 2813 sheet: -0.60 (0.17), residues: 855 loop : -1.17 (0.11), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP w 213 HIS 0.007 0.001 HIS O 43 PHE 0.034 0.001 PHE t 263 TYR 0.035 0.001 TYR t 302 ARG 0.009 0.000 ARG L 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13094 Ramachandran restraints generated. 6547 Oldfield, 0 Emsley, 6547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 525 time to evaluate : 6.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 125 PRO cc_start: 0.7757 (Cg_exo) cc_final: 0.7521 (Cg_endo) REVERT: A 79 SER cc_start: 0.8386 (p) cc_final: 0.8141 (t) REVERT: E 87 MET cc_start: 0.7988 (tpp) cc_final: 0.7660 (tpp) REVERT: I 105 ASP cc_start: 0.7956 (t0) cc_final: 0.7567 (t0) REVERT: I 155 ASN cc_start: 0.7998 (t0) cc_final: 0.7658 (t0) REVERT: J 159 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7508 (t80) REVERT: L 33 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7256 (tt) REVERT: L 91 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7187 (m-30) REVERT: O 37 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6557 (p90) REVERT: O 61 LYS cc_start: 0.7299 (mmtm) cc_final: 0.7091 (mptt) REVERT: O 141 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6666 (ttt90) REVERT: V 1 MET cc_start: 0.7240 (tpp) cc_final: 0.6758 (tpp) REVERT: W 14 ILE cc_start: 0.8685 (pt) cc_final: 0.8291 (mt) REVERT: W 57 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.6624 (mmt-90) REVERT: X 119 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7299 (mmt-90) REVERT: b 65 GLN cc_start: 0.7502 (mm110) cc_final: 0.7142 (mm110) REVERT: x 156 ASP cc_start: 0.7770 (m-30) cc_final: 0.7493 (m-30) REVERT: y 280 MET cc_start: 0.7780 (mmm) cc_final: 0.7392 (mmm) REVERT: u 217 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.6453 (p90) REVERT: u 679 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8028 (pt) REVERT: u 766 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8557 (pp) REVERT: v 244 MET cc_start: 0.1785 (OUTLIER) cc_final: 0.1548 (tpt) outliers start: 113 outliers final: 97 residues processed: 612 average time/residue: 0.7934 time to fit residues: 846.8261 Evaluate side-chains 624 residues out of total 5769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 516 time to evaluate : 6.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 41 MET Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain T residue 137 GLN Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 141 ARG Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 57 ARG Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain x residue 121 CYS Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain y residue 25 LYS Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 130 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 51 VAL Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 223 LEU Chi-restraints excluded: chain u residue 278 VAL Chi-restraints excluded: chain u residue 283 LEU Chi-restraints excluded: chain u residue 359 VAL Chi-restraints excluded: chain u residue 580 ILE Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 260 ASP Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain v residue 112 VAL Chi-restraints excluded: chain v residue 122 LEU Chi-restraints excluded: chain v residue 244 MET Chi-restraints excluded: chain v residue 246 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 511 optimal weight: 5.9990 chunk 686 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 593 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 645 optimal weight: 6.9990 chunk 270 optimal weight: 50.0000 chunk 662 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN F 110 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 ASN ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 71 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.122168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.103882 restraints weight = 207059.074| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.83 r_work: 0.3312 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 92694 Z= 0.362 Angle : 0.704 14.334 132915 Z= 0.353 Chirality : 0.043 0.332 16256 Planarity : 0.005 0.072 10833 Dihedral : 22.532 179.670 32656 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % Rotamer: Outliers : 2.25 % Allowed : 16.34 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.03 % Twisted Proline : 0.35 % Twisted General : 0.02 % 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: 0.02 (0.10), residues: 6547 helix: 1.43 (0.10), residues: 2816 sheet: -0.62 (0.17), residues: 856 loop : -1.23 (0.11), residues: 2875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 390 HIS 0.010 0.001 HIS X 46 PHE 0.035 0.002 PHE X 105 TYR 0.042 0.002 TYR G 28 ARG 0.009 0.001 ARG K 473 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16059.00 seconds wall clock time: 286 minutes 59.94 seconds (17219.94 seconds total)