Starting phenix.real_space_refine on Tue Feb 20 08:46:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtz_32806/02_2024/7wtz_32806.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtz_32806/02_2024/7wtz_32806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtz_32806/02_2024/7wtz_32806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtz_32806/02_2024/7wtz_32806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtz_32806/02_2024/7wtz_32806.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtz_32806/02_2024/7wtz_32806.pdb" } resolution = 3.0 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= 0.012 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 232 5.16 5 C 47509 2.51 5 N 15531 2.21 5 O 20216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 85113 Number of models: 1 Model: "" Number of chains: 36 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': 128, 'rna2p_pyr': 103, 'rna3p_pur': 735, 'rna3p_pyr': 658} Link IDs: {'rna2p': 230, 'rna3p': 1393} 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: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 990 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} 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: "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 68794 SG CYS y 270 111.093 164.361 152.496 1.00 6.21 S ATOM 68814 SG CYS y 273 113.828 164.402 154.134 1.00 6.21 S ATOM 68911 SG CYS y 285 114.377 164.586 150.005 1.00 9.39 S ATOM 68933 SG CYS y 288 113.663 161.482 151.436 1.00 6.21 S Time building chain proxies: 33.24, per 1000 atoms: 0.39 Number of scatterers: 85113 At special positions: 0 Unit cell: (237.216, 247.806, 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 232 16.00 P 1623 15.00 O 20216 8.00 N 15531 7.00 C 47509 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: 33.76 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 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11878 Finding SS restraints... Secondary structure from input PDB file: 245 helices and 48 sheets defined 45.9% alpha, 14.5% beta 524 base pairs and 880 stacking pairs defined. Time for finding SS restraints: 26.17 Creating SS restraints... Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 61 through 66 Processing helix chain 'F' and resid 67 through 75 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 86 through 104 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 142 through 161 Processing helix chain 'F' and resid 168 through 183 Processing helix chain 'F' and resid 187 through 204 Processing helix chain 'M' and resid 13 through 29 removed outlier: 5.106A pdb=" N GLN M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 44 removed outlier: 3.963A pdb=" N LEU M 42 " --> pdb=" O ALA M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 72 removed outlier: 3.714A pdb=" N VAL M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 90 Processing helix chain 'M' and resid 119 through 132 Processing helix chain 'P' and resid 21 through 27 Processing helix chain 'P' and resid 29 through 33 removed outlier: 3.741A pdb=" N GLN P 32 " --> pdb=" O SER P 29 " (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: 3.702A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.709A pdb=" N MET P 111 " --> pdb=" O LYS P 108 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 108 through 112' Processing helix chain 'P' and resid 116 through 120 Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' 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 52 removed outlier: 4.019A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 59 Processing helix chain 'Q' and resid 77 through 99 Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.753A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 39 removed outlier: 3.647A pdb=" N ASN R 31 " --> pdb=" O ASP R 27 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA R 39 " --> pdb=" O CYS R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 64 removed outlier: 3.721A pdb=" N ARG R 47 " --> pdb=" O SER R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 83 removed outlier: 3.674A pdb=" N GLU R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) 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 Processing helix chain 'S' and resid 74 through 78 Processing helix chain 'S' and resid 99 through 118 removed outlier: 3.923A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 128 Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 10 through 26 removed outlier: 3.748A pdb=" N GLY T 26 " --> pdb=" O LEU T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.721A 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 110 removed outlier: 3.584A 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: 3.687A pdb=" N LEU Z 77 " --> pdb=" O VAL Z 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 95 Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.531A pdb=" N GLU A 35 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 4.353A 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: 3.815A pdb=" N GLN A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.763A 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 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.552A pdb=" N ALA A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 57 through 62 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 removed outlier: 3.506A pdb=" N VAL B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 178 removed outlier: 3.992A 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 224 through 233 removed outlier: 4.052A pdb=" N LEU B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 77 through 84 removed outlier: 4.339A pdb=" N ILE C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 4.310A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 207 through 217 Processing helix chain 'C' and resid 232 through 250 removed outlier: 4.759A pdb=" N TYR C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.665A pdb=" N TRP C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS C 257 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.968A 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: 3.685A 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 68 through 75 removed outlier: 3.525A pdb=" N ILE H 75 " --> pdb=" O SER H 71 " (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: 3.705A pdb=" N VAL H 125 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.892A pdb=" N VAL H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 180 Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 88 through 93 removed outlier: 3.847A 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 155 removed outlier: 3.861A 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 192 through 206 Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 61 removed outlier: 4.260A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.500A pdb=" N ILE J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 98 removed outlier: 3.696A pdb=" N ILE J 97 " --> pdb=" O LYS J 93 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU J 98 " --> pdb=" O LEU J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 93 through 98' Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.711A 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 171 through 179 Processing helix chain 'L' and resid 23 through 30 Processing helix chain 'L' and resid 47 through 53 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 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 Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.523A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 84 No H-bonds generated for 'chain 'W' and resid 82 through 84' Processing helix chain 'W' and resid 85 through 94 Processing helix chain 'W' and resid 113 through 119 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 94 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 48 removed outlier: 3.539A pdb=" N ILE Y 40 " --> pdb=" O PRO Y 36 " (cutoff:3.500A) 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: 3.787A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 123 removed outlier: 4.012A 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 'b' and resid 19 through 23 removed outlier: 3.920A pdb=" N ARG b 23 " --> pdb=" O LYS b 20 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 30 through 42 Processing helix chain 'x' and resid 81 through 83 No H-bonds generated for 'chain 'x' and resid 81 through 83' 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 removed outlier: 3.821A pdb=" N HIS x 102 " --> pdb=" O PRO x 98 " (cutoff:3.500A) Processing helix chain 'x' and resid 128 through 143 Processing helix chain 'x' and resid 145 through 155 removed outlier: 4.020A pdb=" N LEU x 152 " --> pdb=" O ASP x 148 " (cutoff:3.500A) Processing helix chain 'x' and resid 166 through 168 No H-bonds generated for 'chain 'x' and resid 166 through 168' 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: 3.974A pdb=" N PHE y 14 " --> pdb=" O ASP y 10 " (cutoff:3.500A) Processing helix chain 'y' and resid 31 through 36 Processing helix chain 'y' and resid 39 through 47 Processing helix chain 'y' and resid 59 through 71 removed outlier: 4.094A pdb=" N VAL y 63 " --> pdb=" O LEU y 59 " (cutoff:3.500A) Processing helix chain 'y' and resid 80 through 98 Processing helix chain 'y' and resid 238 through 249 removed outlier: 3.640A pdb=" N GLN y 242 " --> pdb=" O ASP y 238 " (cutoff:3.500A) Processing helix chain 'y' and resid 380 through 385 removed outlier: 3.627A pdb=" N THR y 384 " --> pdb=" O SER y 380 " (cutoff:3.500A) Processing helix chain 'y' and resid 393 through 399 removed outlier: 3.620A pdb=" N ARG y 397 " --> pdb=" O GLY y 393 " (cutoff:3.500A) Processing helix chain 'u' and resid 49 through 73 Processing helix chain 'u' and resid 95 through 105 removed outlier: 3.924A pdb=" N ALA u 99 " --> pdb=" O SER u 95 " (cutoff:3.500A) removed outlier: 4.087A 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: 4.127A pdb=" N ASP u 202 " --> pdb=" O LYS u 198 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.616A 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 484 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 576 Processing helix chain 'u' and resid 720 through 726 removed outlier: 3.559A pdb=" N LEU u 724 " --> pdb=" O ARG u 720 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 193 Processing helix chain 'w' and resid 201 through 206 removed outlier: 3.631A pdb=" N LYS w 205 " --> pdb=" O PRO w 201 " (cutoff:3.500A) Processing helix chain 'w' and resid 212 through 220 removed outlier: 3.813A pdb=" N ILE w 216 " --> pdb=" O ASN w 212 " (cutoff:3.500A) 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: 3.512A pdb=" N LYS w 288 " --> pdb=" O GLY w 284 " (cutoff:3.500A) Processing helix chain 'w' and resid 290 through 298 removed outlier: 4.032A 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: 3.939A pdb=" N SER w 339 " --> pdb=" O SER w 335 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE w 340 " --> pdb=" O GLY w 336 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE w 341 " --> pdb=" O ALA w 337 " (cutoff:3.500A) Processing helix chain 'w' and resid 353 through 367 Processing helix chain 'w' and resid 375 through 389 removed outlier: 3.581A 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: 4.164A 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: 3.552A pdb=" N GLU K 115 " --> pdb=" O GLN K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 122 removed outlier: 3.899A pdb=" N LYS K 122 " --> pdb=" O SER K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 134 removed outlier: 3.571A pdb=" N GLU K 133 " --> pdb=" O ALA K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 141 removed outlier: 3.517A pdb=" N GLY K 140 " --> pdb=" O SER K 137 " (cutoff:3.500A) removed outlier: 3.700A 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: 5.382A pdb=" N SER K 188 " --> pdb=" O ILE K 184 " (cutoff:3.500A) removed outlier: 5.692A 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: 3.575A pdb=" N THR K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 315 removed outlier: 4.229A 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: 3.535A 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: 4.403A 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 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 Processing helix chain 'K' and resid 463 through 478 removed outlier: 3.552A pdb=" N SER K 467 " --> pdb=" O GLY K 463 " (cutoff:3.500A) Processing helix chain 'K' and resid 486 through 506 removed outlier: 6.961A pdb=" N ARG K 503 " --> pdb=" O GLU K 499 " (cutoff:3.500A) removed outlier: 6.609A 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 543 Processing helix chain 'K' and resid 543 through 551 removed outlier: 4.079A 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 606 removed outlier: 4.090A 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 624 removed outlier: 3.741A 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: 3.566A pdb=" N PHE K 640 " --> pdb=" O VAL K 636 " (cutoff:3.500A) Processing helix chain 'K' and resid 643 through 653 Processing helix chain 'K' and resid 654 through 671 removed outlier: 3.566A pdb=" N ARG K 658 " --> pdb=" O ARG K 654 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL K 659 " --> pdb=" O PRO K 655 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N THR K 660 " --> pdb=" O ASP K 656 " (cutoff:3.500A) Processing helix chain 'K' and resid 675 through 699 removed outlier: 3.866A pdb=" N ARG K 679 " --> pdb=" O ALA K 675 " (cutoff:3.500A) removed outlier: 4.544A 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 Processing helix chain 'K' and resid 725 through 742 Processing helix chain 'K' and resid 746 through 761 Processing helix chain 'K' and resid 762 through 764 No H-bonds generated for 'chain 'K' and resid 762 through 764' Processing helix chain 'K' and resid 765 through 777 Processing helix chain 'K' and resid 778 through 782 removed outlier: 3.681A pdb=" N GLU K 781 " --> pdb=" O PRO K 778 " (cutoff:3.500A) Processing helix chain 'K' and resid 784 through 801 removed outlier: 4.097A pdb=" N SER K 801 " --> pdb=" O GLU K 797 " (cutoff:3.500A) 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 845 removed outlier: 4.071A pdb=" N LYS K 838 " --> pdb=" O ARG K 834 " (cutoff:3.500A) Processing helix chain 'K' and resid 851 through 867 removed outlier: 3.580A 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 928 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: 4.181A pdb=" N LYS K 980 " --> pdb=" O ALA K 976 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS K 981 " --> pdb=" O HIS K 977 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLN K 983 " --> pdb=" O ALA K 979 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU K 984 " --> pdb=" O LYS K 980 " (cutoff:3.500A) removed outlier: 3.809A 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: 3.857A pdb=" N VAL K1020 " --> pdb=" O GLY K1016 " (cutoff:3.500A) Processing helix chain 'K' and resid 1027 through 1042 removed outlier: 3.963A pdb=" N VAL K1031 " --> pdb=" O GLU K1027 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN K1034 " --> pdb=" O ARG K1030 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE K1035 " --> pdb=" O VAL K1031 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG K1036 " --> pdb=" O LEU K1032 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS K1037 " --> pdb=" O VAL K1033 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA K1038 " --> pdb=" O ASN K1034 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 123 through 127 removed outlier: 17.644A pdb=" N ARG F 136 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 12.892A pdb=" N ASN c 45 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ALA F 138 " --> pdb=" O ASN c 45 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS c 47 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP F 140 " --> pdb=" O LYS c 47 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS c 27 " --> pdb=" O ARG c 20 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG c 20 " --> pdb=" O CYS c 27 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN c 29 " --> pdb=" O LEU c 18 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS c 16 " --> pdb=" O ARG c 31 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU c 33 " --> pdb=" O VAL c 14 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL c 14 " --> pdb=" O GLU c 33 " (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: 6.181A pdb=" N VAL P 76 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N TYR P 97 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 7.564A 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 removed outlier: 3.523A pdb=" N LEU Q 31 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE Q 68 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) 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: 6.410A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 106 through 108 Processing sheet with id=AB2, first strand: chain 'f' and resid 132 through 134 Processing sheet with id=AB3, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.987A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.675A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 122 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU A 147 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL A 124 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 43 through 50 removed outlier: 8.456A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N PHE B 100 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 91 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 50 removed outlier: 8.456A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N PHE B 100 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 13.318A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.096A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG B 213 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL B 212 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 102 through 116 removed outlier: 6.522A pdb=" N PHE C 127 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE C 109 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS C 125 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG C 123 " --> pdb=" O PRO C 111 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN C 113 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ARG C 121 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN C 115 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY C 119 " --> pdb=" O GLN C 115 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AB9, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AC1, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.675A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.078A pdb=" N ILE E 136 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL E 131 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR E 159 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE E 172 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN E 161 " --> pdb=" O THR E 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 217 through 221 removed outlier: 3.699A pdb=" N ASN E 197 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS E 233 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.612A pdb=" N ASN G 56 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU G 109 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY G 54 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU G 111 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE G 52 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE G 113 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL G 50 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS G 115 " --> pdb=" O TYR G 48 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR G 48 " --> pdb=" O LYS G 115 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR G 48 " --> pdb=" O ALA G 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AC6, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC7, first strand: chain 'H' and resid 47 through 53 removed outlier: 3.637A pdb=" N VAL H 53 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG H 57 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 184 through 188 removed outlier: 6.957A pdb=" N ARG H 152 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.189A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.332A pdb=" N LYS I 37 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 62 through 67 removed outlier: 7.574A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE I 101 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AD4, first strand: chain 'L' and resid 72 through 79 removed outlier: 16.716A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.758A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 52 through 56 removed outlier: 6.184A pdb=" N LEU O 93 " --> pdb=" O ILE O 126 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG O 128 " --> pdb=" O LEU O 93 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'V' and resid 32 through 39 removed outlier: 4.770A pdb=" N GLN V 49 " --> pdb=" O GLU V 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AD8, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.450A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.498A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LYS X 54 " --> pdb=" O CYS X 69 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N CYS X 69 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY X 56 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ARG X 67 " --> pdb=" O GLY X 56 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 6 through 15 removed outlier: 3.848A pdb=" N VAL Y 24 " --> pdb=" O ARG Y 10 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG Y 20 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AE3, first strand: chain 'b' and resid 64 through 65 Processing sheet with id=AE4, first strand: chain 'x' and resid 75 through 79 removed outlier: 8.514A pdb=" N HIS y 129 " --> pdb=" O ILE x 107 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE x 109 " --> pdb=" O HIS y 129 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'x' and resid 159 through 164 Processing sheet with id=AE6, first strand: chain 'y' and resid 8 through 9 removed outlier: 7.863A pdb=" N VAL y 8 " --> pdb=" O LEU y 235 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'y' and resid 28 through 29 removed outlier: 3.542A pdb=" N THR y 29 " --> pdb=" O ARG y 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'y' and resid 111 through 112 removed outlier: 6.533A 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 113 removed outlier: 6.464A pdb=" N GLN u 84 " --> pdb=" O THR u 155 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU u 157 " --> pdb=" O GLN u 84 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU u 86 " --> pdb=" O LEU u 157 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU u 159 " --> pdb=" O LEU u 86 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL u 88 " --> pdb=" O LEU u 159 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE u 156 " --> pdb=" O THR u 186 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA u 188 " --> pdb=" O ILE u 156 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE u 158 " --> pdb=" O ALA u 188 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'u' and resid 295 through 297 removed outlier: 6.678A pdb=" N ALA u 255 " --> pdb=" O TYR u 277 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR u 277 " --> pdb=" O ALA u 255 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY u 270 " --> pdb=" O GLU u 564 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU u 564 " --> pdb=" O GLY u 270 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N SER u 563 " --> pdb=" O MET u 299 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N MET u 299 " --> pdb=" O SER u 563 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA u 304 " --> pdb=" O LEU u 344 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU u 344 " --> pdb=" O ALA u 304 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'u' and resid 528 through 530 removed outlier: 6.884A pdb=" N GLN u 529 " --> pdb=" O ILE t 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'u' and resid 776 through 780 removed outlier: 6.232A pdb=" N THR u 778 " --> pdb=" O SER u 626 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER u 626 " --> pdb=" O THR u 778 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP u 780 " --> pdb=" O ARG u 624 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS u 669 " --> pdb=" O LEU u 678 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU u 678 " --> pdb=" O LYS u 669 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE u 629 " --> pdb=" O GLN u 641 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYS u 639 " --> pdb=" O GLN u 631 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N HIS u 638 " --> pdb=" O ILE u 694 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG u 696 " --> pdb=" O HIS u 638 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU u 640 " --> pdb=" O ARG u 696 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N VAL u 698 " --> pdb=" O LEU u 640 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE u 741 " --> pdb=" O SER u 754 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER u 754 " --> pdb=" O ILE u 741 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET u 710 " --> pdb=" O ILE u 706 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE u 706 " --> pdb=" O MET u 710 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL u 712 " --> pdb=" O PHE u 704 " (cutoff:3.500A) 2329 hydrogen bonds defined for protein. 6714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1298 hydrogen bonds 2018 hydrogen bond angles 0 basepair planarities 524 basepair parallelities 880 stacking parallelities Total time for adding SS restraints: 72.83 Time building geometry restraints manager: 36.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11928 1.32 - 1.45: 32366 1.45 - 1.58: 42216 1.58 - 1.70: 3232 1.70 - 1.83: 359 Bond restraints: 90101 Sorted by residual: bond pdb=" C TYR K 907 " pdb=" N PRO K 908 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.19e-02 7.06e+03 1.43e+01 bond pdb=" N VAL R 66 " pdb=" CA VAL R 66 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 1.03e+01 bond pdb=" C GLY I 30 " pdb=" N ARG I 31 " ideal model delta sigma weight residual 1.327 1.272 0.054 1.71e-02 3.42e+03 1.01e+01 bond pdb=" CB PRO y 60 " pdb=" CG PRO y 60 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.71e+00 bond pdb=" N ILE R 61 " pdb=" CA ILE R 61 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.44e+00 ... (remaining 90096 not shown) Histogram of bond angle deviations from ideal: 95.64 - 104.55: 7650 104.55 - 113.46: 54549 113.46 - 122.37: 51630 122.37 - 131.28: 15090 131.28 - 140.19: 502 Bond angle restraints: 129421 Sorted by residual: angle pdb=" CA PRO y 60 " pdb=" N PRO y 60 " pdb=" CD PRO y 60 " ideal model delta sigma weight residual 112.00 98.91 13.09 1.40e+00 5.10e-01 8.74e+01 angle pdb=" N GLY B 45 " pdb=" CA GLY B 45 " pdb=" C GLY B 45 " ideal model delta sigma weight residual 110.45 118.64 -8.19 1.30e+00 5.92e-01 3.97e+01 angle pdb=" C GLY X 104 " pdb=" N PHE X 105 " pdb=" CA PHE X 105 " ideal model delta sigma weight residual 122.11 113.07 9.04 1.64e+00 3.72e-01 3.04e+01 angle pdb=" C ASN S 73 " pdb=" CA ASN S 73 " pdb=" CB ASN S 73 " ideal model delta sigma weight residual 110.34 117.24 -6.90 1.30e+00 5.92e-01 2.82e+01 angle pdb=" C LYS X 60 " pdb=" N GLN X 61 " pdb=" CA GLN X 61 " ideal model delta sigma weight residual 121.62 129.77 -8.15 1.57e+00 4.06e-01 2.70e+01 ... (remaining 129416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 52238 35.97 - 71.94: 4305 71.94 - 107.91: 523 107.91 - 143.88: 18 143.88 - 179.85: 25 Dihedral angle restraints: 57109 sinusoidal: 38779 harmonic: 18330 Sorted by residual: dihedral pdb=" O4' U 2 427 " pdb=" C1' U 2 427 " pdb=" N1 U 2 427 " pdb=" C2 U 2 427 " ideal model delta sinusoidal sigma weight residual -160.00 17.73 -177.73 1 1.50e+01 4.44e-03 8.53e+01 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 22.75 177.25 1 1.50e+01 4.44e-03 8.53e+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 200.00 26.50 173.50 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 57106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 14077 0.069 - 0.137: 1563 0.137 - 0.206: 175 0.206 - 0.274: 36 0.274 - 0.343: 20 Chirality restraints: 15871 Sorted by residual: chirality pdb=" CB ILE G 5 " pdb=" CA ILE G 5 " pdb=" CG1 ILE G 5 " pdb=" CG2 ILE G 5 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C1' A 2 25 " pdb=" O4' A 2 25 " pdb=" C2' A 2 25 " pdb=" N9 A 2 25 " both_signs ideal model delta sigma weight residual False 2.46 2.12 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C3' G 21338 " pdb=" C4' G 21338 " pdb=" O3' G 21338 " pdb=" C2' G 21338 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 15868 not shown) Planarity restraints: 10386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 2 509 " -0.031 2.00e-02 2.50e+03 3.10e-02 2.89e+01 pdb=" N9 G 2 509 " 0.008 2.00e-02 2.50e+03 pdb=" C8 G 2 509 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G 2 509 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G 2 509 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G 2 509 " 0.056 2.00e-02 2.50e+03 pdb=" O6 G 2 509 " -0.050 2.00e-02 2.50e+03 pdb=" N1 G 2 509 " -0.031 2.00e-02 2.50e+03 pdb=" C2 G 2 509 " 0.057 2.00e-02 2.50e+03 pdb=" N2 G 2 509 " -0.023 2.00e-02 2.50e+03 pdb=" N3 G 2 509 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G 2 509 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 2 492 " -0.002 2.00e-02 2.50e+03 3.10e-02 2.17e+01 pdb=" N1 C 2 492 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C 2 492 " -0.073 2.00e-02 2.50e+03 pdb=" O2 C 2 492 " 0.052 2.00e-02 2.50e+03 pdb=" N3 C 2 492 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C 2 492 " -0.012 2.00e-02 2.50e+03 pdb=" N4 C 2 492 " 0.010 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=" C LEU y 59 " 0.072 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO y 60 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO y 60 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO y 60 " 0.055 5.00e-02 4.00e+02 ... (remaining 10383 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 10200 2.75 - 3.29: 74705 3.29 - 3.83: 162264 3.83 - 4.36: 194141 4.36 - 4.90: 285796 Nonbonded interactions: 727106 Sorted by model distance: nonbonded pdb=" OP1 U 2 115 " pdb=" O2' C 2 382 " model vdw 2.213 2.440 nonbonded pdb=" N3 U 2 8 " pdb=" N6 A 21196 " model vdw 2.214 3.200 nonbonded pdb=" N LYS f 143 " pdb="ZN ZN f 200 " model vdw 2.225 2.310 nonbonded pdb=" O6 G 21722 " pdb=" O2 U 21812 " model vdw 2.229 2.432 nonbonded pdb=" N6 A 21259 " pdb=" OP1 U 21519 " model vdw 2.233 2.520 ... (remaining 727101 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: 2.680 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: 12.750 Check model and map are aligned: 0.950 Set scattering table: 0.620 Process input model: 247.930 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.260 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:9.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 277.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 : 0.004 0.156 90101 Z= 0.266 Angle : 0.859 16.034 129421 Z= 0.451 Chirality : 0.045 0.343 15871 Planarity : 0.007 0.100 10386 Dihedral : 21.542 179.849 45231 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.91 % Favored : 95.98 % Rotamer: Outliers : 0.09 % Allowed : 0.31 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.02 % 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: -1.27 (0.10), residues: 6239 helix: -0.42 (0.09), residues: 2642 sheet: -0.15 (0.17), residues: 861 loop : -1.40 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP I 67 HIS 0.013 0.001 HIS u 740 PHE 0.035 0.002 PHE x 96 TYR 0.046 0.002 TYR B 205 ARG 0.021 0.001 ARG I 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 829 time to evaluate : 5.487 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: R 29 HIS cc_start: 0.5668 (p90) cc_final: 0.5279 (p90) REVERT: I 4 SER cc_start: 0.6910 (t) cc_final: 0.6580 (p) REVERT: J 10 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7960 (ttm-80) REVERT: L 80 MET cc_start: 0.8251 (mtp) cc_final: 0.7927 (mtm) REVERT: W 90 GLN cc_start: 0.8037 (pt0) cc_final: 0.7826 (pt0) REVERT: X 19 ASP cc_start: 0.7836 (m-30) cc_final: 0.7467 (m-30) REVERT: w 248 ARG cc_start: 0.5455 (mmt180) cc_final: 0.5114 (mmt180) outliers start: 5 outliers final: 3 residues processed: 832 average time/residue: 1.8695 time to fit residues: 2021.8018 Evaluate side-chains 592 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 589 time to evaluate : 5.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain t residue 300 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 659 optimal weight: 7.9990 chunk 591 optimal weight: 5.9990 chunk 328 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 399 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 612 optimal weight: 3.9990 chunk 236 optimal weight: 10.0000 chunk 372 optimal weight: 0.8980 chunk 455 optimal weight: 0.8980 chunk 709 optimal weight: 30.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 137 GLN F 149 GLN R 116 ASN S 73 ASN S 101 ASN c 29 GLN B 43 ASN B 95 ASN B 202 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 HIS E 209 HIS E 214 ASN G 202 ASN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 ASN N 58 HIS V 21 ASN b 65 GLN x 216 GLN ** y 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 218 GLN y 348 GLN u 180 GLN ** u 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 256 HIS ** u 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 501 GLN u 740 HIS w 387 GLN ** t 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 236 GLN ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 90101 Z= 0.250 Angle : 0.652 13.262 129421 Z= 0.332 Chirality : 0.040 0.356 15871 Planarity : 0.005 0.066 10386 Dihedral : 22.848 179.870 32317 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 2.00 % Allowed : 10.60 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.02 % Twisted Proline : 0.00 % 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: -0.41 (0.10), residues: 6239 helix: 0.60 (0.10), residues: 2685 sheet: -0.06 (0.17), residues: 863 loop : -1.20 (0.11), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 67 HIS 0.008 0.001 HIS u 676 PHE 0.033 0.002 PHE y 69 TYR 0.023 0.002 TYR F 56 ARG 0.009 0.001 ARG Q 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 644 time to evaluate : 5.659 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: symmetry clash REVERT: M 12 MET cc_start: 0.0996 (pmt) cc_final: -0.0440 (tmt) REVERT: A 177 MET cc_start: 0.8323 (mtt) cc_final: 0.8021 (mtt) REVERT: A 185 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8073 (mtt) REVERT: C 105 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: C 242 ASP cc_start: 0.7529 (t0) cc_final: 0.7217 (t0) REVERT: G 63 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7919 (ptm) REVERT: H 162 GLN cc_start: 0.6690 (mp10) cc_final: 0.6456 (mp10) REVERT: J 58 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7213 (mtp180) REVERT: L 80 MET cc_start: 0.8398 (mtp) cc_final: 0.8059 (mtm) REVERT: V 62 MET cc_start: 0.7430 (tpp) cc_final: 0.6849 (tpp) REVERT: W 90 GLN cc_start: 0.8429 (pt0) cc_final: 0.8095 (pt0) REVERT: X 19 ASP cc_start: 0.7774 (m-30) cc_final: 0.7407 (m-30) REVERT: X 36 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7968 (tm) REVERT: Y 74 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8300 (mtp) REVERT: b 5 LYS cc_start: 0.5559 (OUTLIER) cc_final: 0.4692 (tttm) REVERT: w 248 ARG cc_start: 0.5735 (mmt180) cc_final: 0.5061 (mmt180) outliers start: 109 outliers final: 42 residues processed: 687 average time/residue: 1.7369 time to fit residues: 1590.3595 Evaluate side-chains 620 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 571 time to evaluate : 5.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 127 TRP Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain J residue 58 ARG Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain V residue 74 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain b residue 5 LYS Chi-restraints excluded: chain e residue 22 GLN Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain y residue 68 GLU Chi-restraints excluded: chain y residue 234 CYS Chi-restraints excluded: chain y residue 409 VAL Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 591 MET Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain w residue 301 THR Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain K residue 510 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 394 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 590 optimal weight: 5.9990 chunk 482 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 710 optimal weight: 9.9990 chunk 767 optimal weight: 10.0000 chunk 632 optimal weight: 1.9990 chunk 704 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 chunk 569 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 GLN Q 80 GLN R 29 HIS S 101 ASN A 113 GLN B 95 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN y 92 GLN u 63 GLN u 74 GLN ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 256 HIS w 232 GLN w 240 ASN w 387 GLN w 408 GLN ** t 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 886 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 90101 Z= 0.384 Angle : 0.737 13.187 129421 Z= 0.372 Chirality : 0.044 0.406 15871 Planarity : 0.006 0.098 10386 Dihedral : 22.878 179.182 32313 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.90 % Rotamer: Outliers : 2.91 % Allowed : 14.14 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.02 % Twisted Proline : 0.00 % 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: -0.23 (0.10), residues: 6239 helix: 0.81 (0.10), residues: 2690 sheet: -0.11 (0.17), residues: 890 loop : -1.13 (0.11), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP w 213 HIS 0.010 0.002 HIS u 676 PHE 0.035 0.002 PHE y 69 TYR 0.022 0.002 TYR K 720 ARG 0.009 0.001 ARG T 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 607 time to evaluate : 5.621 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: M 12 MET cc_start: 0.1069 (pmt) cc_final: -0.0116 (tmt) REVERT: C 105 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: C 114 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6717 (mtpm) REVERT: C 176 LYS cc_start: 0.7673 (mmpt) cc_final: 0.7467 (mmmt) REVERT: C 248 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.6829 (t80) REVERT: G 1 MET cc_start: 0.5740 (tmm) cc_final: 0.4907 (ttt) REVERT: G 63 MET cc_start: 0.8364 (ptt) cc_final: 0.8083 (ptm) REVERT: I 4 SER cc_start: 0.7180 (t) cc_final: 0.6828 (p) REVERT: J 156 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6731 (p-80) REVERT: L 80 MET cc_start: 0.8571 (mtp) cc_final: 0.8258 (mtm) REVERT: O 37 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6137 (p90) REVERT: W 47 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7443 (tp) REVERT: X 19 ASP cc_start: 0.7738 (m-30) cc_final: 0.7395 (m-30) REVERT: Y 74 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8009 (mtp) REVERT: Y 84 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7496 (mtmt) REVERT: u 198 LYS cc_start: 0.5252 (tttp) cc_final: 0.4414 (tppt) REVERT: u 297 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.6528 (p90) REVERT: w 248 ARG cc_start: 0.5916 (mmt180) cc_final: 0.5215 (mpt180) outliers start: 159 outliers final: 74 residues processed: 688 average time/residue: 1.6855 time to fit residues: 1563.2932 Evaluate side-chains 642 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 559 time to evaluate : 5.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 127 TRP Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 61 SER Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 181 GLN Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain N residue 138 ASN Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain V residue 74 LYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 68 GLU Chi-restraints excluded: chain y residue 214 ILE Chi-restraints excluded: chain y residue 234 CYS Chi-restraints excluded: chain y residue 409 VAL Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 591 MET Chi-restraints excluded: chain u residue 636 ASP Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain w residue 301 THR Chi-restraints excluded: chain w residue 313 THR Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 510 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 701 optimal weight: 30.0000 chunk 534 optimal weight: 7.9990 chunk 368 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 339 optimal weight: 0.2980 chunk 477 optimal weight: 3.9990 chunk 713 optimal weight: 6.9990 chunk 754 optimal weight: 8.9990 chunk 372 optimal weight: 4.9990 chunk 675 optimal weight: 8.9990 chunk 203 optimal weight: 0.9980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 GLN S 101 ASN f 135 HIS B 43 ASN B 53 GLN B 95 ASN I 88 ASN ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 190 GLN ** u 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 256 HIS w 387 GLN w 408 GLN ** t 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 90101 Z= 0.300 Angle : 0.669 11.816 129421 Z= 0.340 Chirality : 0.041 0.373 15871 Planarity : 0.005 0.082 10386 Dihedral : 22.799 179.984 32311 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 3.37 % Allowed : 16.04 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.02 % Twisted Proline : 0.00 % 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: -0.05 (0.11), residues: 6239 helix: 1.03 (0.10), residues: 2683 sheet: -0.14 (0.17), residues: 877 loop : -1.06 (0.12), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP w 213 HIS 0.008 0.001 HIS u 676 PHE 0.043 0.002 PHE K 353 TYR 0.035 0.002 TYR Q 99 ARG 0.006 0.001 ARG O 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 605 time to evaluate : 5.439 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 12 MET cc_start: 0.1452 (pmt) cc_final: 0.0380 (tmt) REVERT: Q 99 TYR cc_start: 0.6582 (m-10) cc_final: 0.6083 (m-10) REVERT: Q 117 ARG cc_start: 0.4871 (OUTLIER) cc_final: 0.4598 (ppt170) REVERT: B 227 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6551 (tptp) REVERT: C 105 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: C 114 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6774 (mtpm) REVERT: C 232 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7566 (p) REVERT: C 242 ASP cc_start: 0.7641 (t0) cc_final: 0.7333 (t0) REVERT: G 63 MET cc_start: 0.8417 (ptt) cc_final: 0.8006 (ptm) REVERT: I 4 SER cc_start: 0.7120 (t) cc_final: 0.6806 (p) REVERT: I 88 ASN cc_start: 0.7092 (OUTLIER) cc_final: 0.6627 (t0) REVERT: I 181 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8125 (pt0) REVERT: I 205 ARG cc_start: 0.7655 (tpp80) cc_final: 0.6911 (ttt180) REVERT: J 59 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7348 (tm-30) REVERT: J 156 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.6759 (p-80) REVERT: L 80 MET cc_start: 0.8540 (mtp) cc_final: 0.8221 (mtm) REVERT: L 104 LYS cc_start: 0.8190 (tptm) cc_final: 0.7723 (tptp) REVERT: O 37 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.6183 (p90) REVERT: W 47 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7397 (tp) REVERT: X 19 ASP cc_start: 0.7707 (m-30) cc_final: 0.7363 (m-30) REVERT: X 119 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8162 (mtt90) REVERT: Y 16 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7750 (ttm110) REVERT: Y 74 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7973 (mtp) REVERT: Y 84 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7408 (mtmt) REVERT: b 65 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: u 198 LYS cc_start: 0.5261 (tttp) cc_final: 0.4451 (tppt) REVERT: u 297 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.6555 (p90) REVERT: w 248 ARG cc_start: 0.6005 (mmt180) cc_final: 0.5447 (mpt180) REVERT: K 117 ASN cc_start: -0.0860 (OUTLIER) cc_final: -0.2234 (t0) outliers start: 184 outliers final: 78 residues processed: 714 average time/residue: 1.6382 time to fit residues: 1576.2291 Evaluate side-chains 667 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 573 time to evaluate : 5.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain Q residue 117 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 127 TRP Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 181 GLN Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain V residue 74 LYS Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain b residue 65 GLN Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 40 ARG Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 234 CYS Chi-restraints excluded: chain y residue 285 CYS Chi-restraints excluded: chain y residue 306 LEU Chi-restraints excluded: chain y residue 409 VAL Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 190 GLN Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 591 MET Chi-restraints excluded: chain u residue 636 ASP Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 675 MET Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain w residue 301 THR Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 510 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 628 optimal weight: 10.0000 chunk 428 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 562 optimal weight: 40.0000 chunk 311 optimal weight: 0.9980 chunk 644 optimal weight: 6.9990 chunk 521 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 385 optimal weight: 2.9990 chunk 677 optimal weight: 2.9990 chunk 190 optimal weight: 50.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 101 ASN B 95 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 ASN ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 GLN ** y 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 74 GLN ** u 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 256 HIS u 301 GLN u 356 GLN w 387 GLN w 408 GLN t 299 ASN ** t 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 811 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 90101 Z= 0.229 Angle : 0.622 12.687 129421 Z= 0.317 Chirality : 0.039 0.342 15871 Planarity : 0.005 0.063 10386 Dihedral : 22.731 179.938 32311 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 3.24 % Allowed : 17.33 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.02 % 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: 0.09 (0.11), residues: 6239 helix: 1.21 (0.10), residues: 2684 sheet: -0.19 (0.17), residues: 883 loop : -1.02 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP w 213 HIS 0.007 0.001 HIS O 43 PHE 0.035 0.002 PHE K 353 TYR 0.027 0.001 TYR R 20 ARG 0.008 0.000 ARG O 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 604 time to evaluate : 5.660 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 12 MET cc_start: 0.1428 (pmt) cc_final: 0.0448 (tmt) REVERT: P 53 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7397 (mp10) REVERT: C 105 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: C 114 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6676 (mtpm) REVERT: C 242 ASP cc_start: 0.7581 (t0) cc_final: 0.7295 (t0) REVERT: G 63 MET cc_start: 0.8421 (ptt) cc_final: 0.7996 (ptm) REVERT: I 4 SER cc_start: 0.7096 (t) cc_final: 0.6791 (p) REVERT: I 89 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: J 10 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.7985 (ttm-80) REVERT: J 59 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7295 (tm-30) REVERT: J 143 ASN cc_start: 0.7862 (t0) cc_final: 0.7591 (t0) REVERT: J 156 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.6809 (p-80) REVERT: L 80 MET cc_start: 0.8507 (mtp) cc_final: 0.8174 (mtm) REVERT: L 104 LYS cc_start: 0.8208 (tptm) cc_final: 0.7768 (tptp) REVERT: N 133 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7197 (ttm-80) REVERT: O 37 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6080 (p90) REVERT: W 41 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8891 (mtp) REVERT: W 47 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7358 (tp) REVERT: X 19 ASP cc_start: 0.7695 (m-30) cc_final: 0.7359 (m-30) REVERT: X 119 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8161 (mtt90) REVERT: Y 16 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7695 (ttm170) REVERT: Y 74 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7920 (mtp) REVERT: Y 84 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7327 (mtmt) REVERT: b 65 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: u 198 LYS cc_start: 0.5267 (tttp) cc_final: 0.4424 (tppt) REVERT: u 297 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.6527 (p90) outliers start: 177 outliers final: 88 residues processed: 714 average time/residue: 1.6841 time to fit residues: 1625.6617 Evaluate side-chains 668 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 566 time to evaluate : 5.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain P residue 53 GLN Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 127 TRP Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain N residue 70 LYS Chi-restraints excluded: chain N residue 133 ARG Chi-restraints excluded: chain N residue 138 ASN Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain b residue 56 CYS Chi-restraints excluded: chain b residue 65 GLN Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain e residue 40 ARG Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 207 VAL Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 234 CYS Chi-restraints excluded: chain y residue 285 CYS Chi-restraints excluded: chain y residue 306 LEU Chi-restraints excluded: chain y residue 409 VAL Chi-restraints excluded: chain u residue 100 MET Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 591 MET Chi-restraints excluded: chain u residue 636 ASP Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 675 MET Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 716 MET Chi-restraints excluded: chain w residue 301 THR Chi-restraints excluded: chain w residue 404 LEU Chi-restraints excluded: chain t residue 250 MET Chi-restraints excluded: chain t residue 466 LEU Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 380 SER Chi-restraints excluded: chain K residue 510 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 253 optimal weight: 9.9990 chunk 679 optimal weight: 0.0670 chunk 149 optimal weight: 10.0000 chunk 443 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 755 optimal weight: 40.0000 chunk 627 optimal weight: 6.9990 chunk 349 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 249 optimal weight: 4.9990 chunk 396 optimal weight: 5.9990 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN Q 24 HIS S 101 ASN T 105 GLN B 95 ASN C 235 ASN H 33 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 ASN I 181 GLN J 111 GLN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN ** y 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 190 GLN ** u 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 256 HIS ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 408 GLN ** t 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 90101 Z= 0.422 Angle : 0.771 14.073 129421 Z= 0.386 Chirality : 0.046 0.415 15871 Planarity : 0.006 0.107 10386 Dihedral : 22.828 179.109 32311 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.54 % Rotamer: Outliers : 3.99 % Allowed : 18.15 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.02 % 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 (0.11), residues: 6239 helix: 1.06 (0.10), residues: 2705 sheet: -0.13 (0.17), residues: 868 loop : -1.09 (0.12), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP w 213 HIS 0.009 0.002 HIS J 156 PHE 0.029 0.002 PHE K 353 TYR 0.028 0.002 TYR Q 82 ARG 0.009 0.001 ARG O 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 605 time to evaluate : 6.305 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: symmetry clash revert: symmetry clash REVERT: M 12 MET cc_start: 0.1476 (pmt) cc_final: 0.0661 (tmt) REVERT: P 53 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7309 (mt0) REVERT: P 64 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7298 (ttpp) REVERT: Q 117 ARG cc_start: 0.4898 (OUTLIER) cc_final: 0.4659 (ppt170) REVERT: R 78 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.5645 (ptm160) REVERT: c 67 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.5472 (ptp-170) REVERT: B 227 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6506 (tppp) REVERT: C 105 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: C 114 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6977 (mtpm) REVERT: C 248 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.6864 (t80) REVERT: E 222 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8103 (tp) REVERT: G 91 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: H 76 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.6732 (tt0) REVERT: H 138 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7306 (pt0) REVERT: I 4 SER cc_start: 0.7138 (t) cc_final: 0.6860 (p) REVERT: I 89 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: J 152 ASP cc_start: 0.7078 (p0) cc_final: 0.6848 (p0) REVERT: J 156 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6420 (p-80) REVERT: L 19 ASN cc_start: 0.7578 (m-40) cc_final: 0.7359 (m110) REVERT: L 80 MET cc_start: 0.8635 (mtp) cc_final: 0.8373 (mtm) REVERT: L 104 LYS cc_start: 0.8232 (tptm) cc_final: 0.7850 (tptp) REVERT: N 133 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7132 (ttm-80) REVERT: O 37 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6442 (p90) REVERT: O 142 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7420 (ttm-80) REVERT: W 41 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8842 (ttt) REVERT: W 47 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7494 (tp) REVERT: X 19 ASP cc_start: 0.7743 (m-30) cc_final: 0.7405 (m-30) REVERT: X 119 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8166 (mtt90) REVERT: Y 16 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7785 (ttm170) REVERT: Y 74 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7932 (mtp) REVERT: Y 84 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7447 (mtmt) REVERT: b 65 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: u 61 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.6500 (ttm-80) REVERT: u 198 LYS cc_start: 0.5432 (tttp) cc_final: 0.4573 (tppt) REVERT: u 297 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6506 (p90) REVERT: K 117 ASN cc_start: -0.0866 (OUTLIER) cc_final: -0.2403 (t0) REVERT: K 542 MET cc_start: 0.4633 (mmt) cc_final: 0.4257 (mmm) outliers start: 218 outliers final: 99 residues processed: 744 average time/residue: 1.6985 time to fit residues: 1689.4484 Evaluate side-chains 692 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 566 time to evaluate : 5.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain P residue 53 GLN Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 64 LYS Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 117 ARG Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 127 TRP Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 67 ARG Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 133 ARG Chi-restraints excluded: chain N residue 138 ASN Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 142 ARG Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 47 MET Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain b residue 56 CYS Chi-restraints excluded: chain b residue 65 GLN Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 234 CYS Chi-restraints excluded: chain y residue 285 CYS Chi-restraints excluded: chain y residue 306 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 409 VAL Chi-restraints excluded: chain u residue 61 ARG Chi-restraints excluded: chain u residue 100 MET Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 591 MET Chi-restraints excluded: chain u residue 636 ASP Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 675 MET Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain w residue 301 THR Chi-restraints excluded: chain w residue 404 LEU Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 466 LEU Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 380 SER Chi-restraints excluded: chain K residue 510 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 728 optimal weight: 30.0000 chunk 85 optimal weight: 5.9990 chunk 430 optimal weight: 3.9990 chunk 551 optimal weight: 0.6980 chunk 427 optimal weight: 0.8980 chunk 636 optimal weight: 1.9990 chunk 421 optimal weight: 1.9990 chunk 752 optimal weight: 20.0000 chunk 471 optimal weight: 0.9980 chunk 458 optimal weight: 0.8980 chunk 347 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 11 HIS ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 ASN B 95 ASN C 235 ASN E 67 GLN ** G 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 ASN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 GLN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 190 GLN ** u 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 235 GLN u 256 HIS ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 401 GLN u 631 GLN ** w 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 408 GLN w 422 GLN t 299 ASN t 469 ASN ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 90101 Z= 0.160 Angle : 0.596 12.138 129421 Z= 0.303 Chirality : 0.037 0.287 15871 Planarity : 0.004 0.052 10386 Dihedral : 22.673 179.911 32311 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.67 % Rotamer: Outliers : 2.93 % Allowed : 19.49 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.02 % 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: 0.27 (0.11), residues: 6239 helix: 1.37 (0.10), residues: 2684 sheet: -0.13 (0.17), residues: 877 loop : -0.92 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP w 213 HIS 0.008 0.001 HIS O 43 PHE 0.026 0.001 PHE K 353 TYR 0.026 0.001 TYR Q 99 ARG 0.011 0.000 ARG Z 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 606 time to evaluate : 8.416 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 12 MET cc_start: 0.1245 (pmt) cc_final: 0.0626 (tmt) REVERT: Q 117 ARG cc_start: 0.4765 (OUTLIER) cc_final: 0.4548 (ppt170) REVERT: B 227 LYS cc_start: 0.6759 (OUTLIER) cc_final: 0.6473 (tppp) REVERT: C 114 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6693 (mtpm) REVERT: C 242 ASP cc_start: 0.7402 (t0) cc_final: 0.7162 (t0) REVERT: H 138 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7305 (pt0) REVERT: I 4 SER cc_start: 0.7026 (t) cc_final: 0.6758 (p) REVERT: J 103 GLU cc_start: 0.7978 (mp0) cc_final: 0.7718 (mp0) REVERT: J 156 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6775 (p-80) REVERT: L 80 MET cc_start: 0.8454 (mtp) cc_final: 0.8120 (mtm) REVERT: L 104 LYS cc_start: 0.8190 (tptm) cc_final: 0.7903 (tptp) REVERT: O 37 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.6101 (p90) REVERT: V 62 MET cc_start: 0.7367 (tpp) cc_final: 0.6704 (tpp) REVERT: W 47 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7419 (tp) REVERT: W 90 GLN cc_start: 0.8516 (pt0) cc_final: 0.8219 (pt0) REVERT: X 19 ASP cc_start: 0.7652 (m-30) cc_final: 0.7331 (m-30) REVERT: X 119 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8130 (mtt90) REVERT: Y 16 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7638 (ttm170) REVERT: u 61 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.6364 (ttm-80) REVERT: u 198 LYS cc_start: 0.5215 (tttp) cc_final: 0.4355 (tppt) REVERT: u 297 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6693 (p90) REVERT: K 117 ASN cc_start: -0.0798 (OUTLIER) cc_final: -0.2347 (t0) REVERT: K 542 MET cc_start: 0.4657 (mmt) cc_final: 0.4214 (mmm) outliers start: 160 outliers final: 68 residues processed: 710 average time/residue: 1.6761 time to fit residues: 1608.6752 Evaluate side-chains 654 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 575 time to evaluate : 5.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain Q residue 13 PHE Chi-restraints excluded: chain Q residue 117 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 127 TRP Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 56 CYS Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 285 CYS Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 61 ARG Chi-restraints excluded: chain u residue 100 MET Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 344 LEU Chi-restraints excluded: chain u residue 549 VAL Chi-restraints excluded: chain u residue 591 MET Chi-restraints excluded: chain u residue 675 MET Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 745 LEU Chi-restraints excluded: chain t residue 251 ARG Chi-restraints excluded: chain t residue 300 ASP Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 339 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 465 optimal weight: 6.9990 chunk 300 optimal weight: 9.9990 chunk 449 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 147 optimal weight: 40.0000 chunk 145 optimal weight: 10.0000 chunk 478 optimal weight: 0.8980 chunk 512 optimal weight: 1.9990 chunk 372 optimal weight: 8.9990 chunk 70 optimal weight: 50.0000 chunk 591 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 GLN ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 ASN Z 106 GLN B 43 ASN B 95 ASN B 208 HIS C 235 ASN E 67 GLN G 65 GLN G 70 HIS G 155 GLN ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 ASN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN x 210 HIS u 190 GLN ** u 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 256 HIS ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 408 GLN t 469 ASN ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 90101 Z= 0.313 Angle : 0.691 13.902 129421 Z= 0.347 Chirality : 0.042 0.381 15871 Planarity : 0.005 0.090 10386 Dihedral : 22.689 179.492 32311 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 2.93 % Allowed : 20.18 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.11), residues: 6239 helix: 1.28 (0.10), residues: 2696 sheet: -0.08 (0.17), residues: 858 loop : -0.97 (0.12), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP w 213 HIS 0.006 0.001 HIS y 271 PHE 0.026 0.002 PHE w 204 TYR 0.032 0.002 TYR Q 99 ARG 0.019 0.001 ARG y 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 596 time to evaluate : 5.525 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 12 MET cc_start: 0.1471 (pmt) cc_final: 0.0727 (tmt) REVERT: Q 117 ARG cc_start: 0.4915 (OUTLIER) cc_final: 0.4502 (ppt170) REVERT: R 78 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.5452 (ptm160) REVERT: B 227 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6409 (tptp) REVERT: C 105 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: C 114 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6732 (mtpm) REVERT: C 242 ASP cc_start: 0.7641 (t0) cc_final: 0.7377 (t0) REVERT: C 248 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7082 (t80) REVERT: G 91 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: H 138 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7296 (pt0) REVERT: I 4 SER cc_start: 0.7073 (t) cc_final: 0.6801 (p) REVERT: J 103 GLU cc_start: 0.8040 (mp0) cc_final: 0.7742 (mp0) REVERT: J 143 ASN cc_start: 0.8129 (t0) cc_final: 0.7851 (t0) REVERT: J 152 ASP cc_start: 0.7032 (p0) cc_final: 0.6733 (p0) REVERT: J 156 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6621 (p-80) REVERT: L 80 MET cc_start: 0.8619 (mtp) cc_final: 0.8302 (mtm) REVERT: L 104 LYS cc_start: 0.8315 (tptm) cc_final: 0.7932 (tptp) REVERT: O 37 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6352 (p90) REVERT: W 47 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7429 (tp) REVERT: X 19 ASP cc_start: 0.7700 (m-30) cc_final: 0.7370 (m-30) REVERT: X 119 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8193 (mtt90) REVERT: Y 16 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7765 (ttm170) REVERT: b 15 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: b 65 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7144 (mp10) REVERT: e 5 SER cc_start: 0.6867 (m) cc_final: 0.6434 (m) REVERT: u 61 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.6447 (ttm-80) REVERT: u 198 LYS cc_start: 0.5418 (tttp) cc_final: 0.4540 (tppt) REVERT: u 297 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6485 (p90) REVERT: K 117 ASN cc_start: -0.0807 (OUTLIER) cc_final: -0.2435 (t0) outliers start: 160 outliers final: 83 residues processed: 710 average time/residue: 1.6225 time to fit residues: 1555.7903 Evaluate side-chains 676 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 576 time to evaluate : 5.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain Q residue 13 PHE Chi-restraints excluded: chain Q residue 117 ARG Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 127 TRP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 56 CYS Chi-restraints excluded: chain b residue 65 GLN Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 202 ILE Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 285 CYS Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 61 ARG Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain u residue 100 MET Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 549 VAL Chi-restraints excluded: chain u residue 560 LEU Chi-restraints excluded: chain u residue 591 MET Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 675 MET Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 745 LEU Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 251 ARG Chi-restraints excluded: chain t residue 300 ASP Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 349 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 684 optimal weight: 0.6980 chunk 721 optimal weight: 20.0000 chunk 657 optimal weight: 0.6980 chunk 701 optimal weight: 30.0000 chunk 720 optimal weight: 0.7980 chunk 422 optimal weight: 0.7980 chunk 305 optimal weight: 1.9990 chunk 550 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 633 optimal weight: 4.9990 chunk 663 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN S 101 ASN Z 106 GLN B 95 ASN C 235 ASN E 67 GLN ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 ASN I 146 GLN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN ** u 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 256 HIS ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 408 GLN t 299 ASN t 469 ASN ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 90101 Z= 0.152 Angle : 0.601 17.612 129421 Z= 0.303 Chirality : 0.036 0.271 15871 Planarity : 0.004 0.073 10386 Dihedral : 22.605 179.915 32311 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.44 % Rotamer: Outliers : 2.20 % Allowed : 21.06 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.11), residues: 6239 helix: 1.44 (0.10), residues: 2688 sheet: -0.15 (0.17), residues: 869 loop : -0.87 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP u 133 HIS 0.007 0.001 HIS u 144 PHE 0.028 0.001 PHE w 204 TYR 0.027 0.001 TYR t 301 ARG 0.013 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 615 time to evaluate : 5.591 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 12 MET cc_start: 0.1544 (pmt) cc_final: 0.0677 (tmt) REVERT: Q 33 LYS cc_start: 0.6400 (mmmt) cc_final: 0.6190 (mmpt) REVERT: Q 117 ARG cc_start: 0.4899 (OUTLIER) cc_final: 0.4505 (ppt170) REVERT: R 78 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.5375 (ptm160) REVERT: A 155 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8420 (ttp-170) REVERT: C 114 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6685 (mtpm) REVERT: C 242 ASP cc_start: 0.7393 (t0) cc_final: 0.7141 (t0) REVERT: C 248 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.6933 (t80) REVERT: G 91 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: G 124 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7061 (tt) REVERT: H 138 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7265 (pt0) REVERT: I 4 SER cc_start: 0.6987 (t) cc_final: 0.6717 (p) REVERT: I 110 ARG cc_start: 0.7882 (tmm-80) cc_final: 0.7525 (ttp80) REVERT: J 143 ASN cc_start: 0.7989 (t0) cc_final: 0.7787 (t0) REVERT: L 39 ASN cc_start: 0.7492 (t0) cc_final: 0.7070 (p0) REVERT: L 80 MET cc_start: 0.8443 (mtp) cc_final: 0.8119 (mtm) REVERT: L 104 LYS cc_start: 0.8172 (tptm) cc_final: 0.7900 (tptp) REVERT: O 37 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.5979 (p90) REVERT: O 142 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7356 (ttm-80) REVERT: V 62 MET cc_start: 0.7386 (tpp) cc_final: 0.6784 (tpp) REVERT: W 90 GLN cc_start: 0.8515 (pt0) cc_final: 0.8205 (pt0) REVERT: X 19 ASP cc_start: 0.7656 (m-30) cc_final: 0.7338 (m-30) REVERT: X 119 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8144 (mtt90) REVERT: Y 16 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7679 (ttm170) REVERT: e 5 SER cc_start: 0.6921 (m) cc_final: 0.6554 (m) REVERT: u 61 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.6375 (ttm-80) REVERT: u 198 LYS cc_start: 0.5082 (tttp) cc_final: 0.4262 (tppt) REVERT: u 297 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.6662 (p90) REVERT: u 743 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6654 (tm-30) REVERT: K 117 ASN cc_start: -0.0759 (OUTLIER) cc_final: -0.2388 (t0) REVERT: K 542 MET cc_start: 0.4144 (mmt) cc_final: 0.3722 (mmm) outliers start: 120 outliers final: 67 residues processed: 705 average time/residue: 1.6376 time to fit residues: 1561.5639 Evaluate side-chains 663 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 582 time to evaluate : 5.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain Q residue 13 PHE Chi-restraints excluded: chain Q residue 117 ARG Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 127 TRP Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 142 ARG Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 56 CYS Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 207 VAL Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 285 CYS Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 61 ARG Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 549 VAL Chi-restraints excluded: chain u residue 560 LEU Chi-restraints excluded: chain u residue 591 MET Chi-restraints excluded: chain u residue 636 ASP Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 745 LEU Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 251 ARG Chi-restraints excluded: chain t residue 300 ASP Chi-restraints excluded: chain t residue 426 ASP Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 349 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 699 optimal weight: 8.9990 chunk 460 optimal weight: 0.9980 chunk 741 optimal weight: 9.9990 chunk 452 optimal weight: 2.9990 chunk 351 optimal weight: 0.9990 chunk 515 optimal weight: 1.9990 chunk 778 optimal weight: 10.0000 chunk 716 optimal weight: 2.9990 chunk 619 optimal weight: 0.0670 chunk 64 optimal weight: 6.9990 chunk 478 optimal weight: 4.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN S 101 ASN S 125 HIS ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 208 HIS C 235 ASN E 67 GLN H 163 GLN H 165 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 GLN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN u 226 GLN ** u 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 256 HIS ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 232 GLN ** w 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 408 GLN t 469 ASN ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 90101 Z= 0.178 Angle : 0.613 14.679 129421 Z= 0.307 Chirality : 0.037 0.290 15871 Planarity : 0.004 0.080 10386 Dihedral : 22.555 179.427 32311 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 1.76 % Allowed : 21.65 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.11), residues: 6239 helix: 1.48 (0.10), residues: 2683 sheet: -0.12 (0.17), residues: 872 loop : -0.86 (0.12), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP w 213 HIS 0.008 0.001 HIS u 144 PHE 0.029 0.001 PHE w 204 TYR 0.021 0.001 TYR K 720 ARG 0.015 0.000 ARG J 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12478 Ramachandran restraints generated. 6239 Oldfield, 0 Emsley, 6239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 591 time to evaluate : 5.567 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 168 THR cc_start: 0.7771 (p) cc_final: 0.7536 (m) REVERT: M 12 MET cc_start: 0.1555 (pmt) cc_final: 0.0680 (tmt) REVERT: Q 117 ARG cc_start: 0.4905 (OUTLIER) cc_final: 0.4504 (ppt170) REVERT: R 78 ARG cc_start: 0.6250 (OUTLIER) cc_final: 0.5390 (ptm160) REVERT: C 114 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6697 (mtpm) REVERT: C 176 LYS cc_start: 0.7765 (mmpt) cc_final: 0.7551 (mmmt) REVERT: C 242 ASP cc_start: 0.7470 (t0) cc_final: 0.7223 (t0) REVERT: C 248 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7000 (t80) REVERT: G 1 MET cc_start: 0.7788 (tmm) cc_final: 0.7496 (ttt) REVERT: G 63 MET cc_start: 0.8382 (ptm) cc_final: 0.7879 (ptm) REVERT: G 91 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: H 138 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: I 4 SER cc_start: 0.7004 (t) cc_final: 0.6709 (p) REVERT: I 110 ARG cc_start: 0.7883 (tmm-80) cc_final: 0.7523 (ttp80) REVERT: J 143 ASN cc_start: 0.8041 (t0) cc_final: 0.7837 (t0) REVERT: J 152 ASP cc_start: 0.6985 (p0) cc_final: 0.6757 (p0) REVERT: L 80 MET cc_start: 0.8516 (mtp) cc_final: 0.8144 (mtm) REVERT: L 104 LYS cc_start: 0.8230 (tptm) cc_final: 0.7962 (tptp) REVERT: O 37 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6125 (p90) REVERT: O 60 MET cc_start: 0.7697 (ptm) cc_final: 0.7433 (ptp) REVERT: O 142 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7367 (ttm-80) REVERT: V 62 MET cc_start: 0.7380 (tpp) cc_final: 0.6751 (tpp) REVERT: W 90 GLN cc_start: 0.8516 (pt0) cc_final: 0.8197 (pt0) REVERT: X 19 ASP cc_start: 0.7685 (m-30) cc_final: 0.7355 (m-30) REVERT: X 119 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8179 (mtt90) REVERT: Y 16 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7716 (ttm170) REVERT: e 5 SER cc_start: 0.6919 (OUTLIER) cc_final: 0.6539 (m) REVERT: u 61 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.6372 (ttm-80) REVERT: u 198 LYS cc_start: 0.5124 (tttp) cc_final: 0.4304 (tppt) REVERT: u 297 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6500 (p90) REVERT: w 248 ARG cc_start: 0.6348 (mpt180) cc_final: 0.6148 (mmt180) REVERT: t 469 ASN cc_start: 0.6049 (OUTLIER) cc_final: 0.5518 (p0) REVERT: K 117 ASN cc_start: -0.0746 (OUTLIER) cc_final: -0.2404 (t0) REVERT: K 542 MET cc_start: 0.4238 (mmt) cc_final: 0.3789 (mmm) outliers start: 96 outliers final: 66 residues processed: 664 average time/residue: 1.6775 time to fit residues: 1504.1108 Evaluate side-chains 657 residues out of total 5482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 577 time to evaluate : 5.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain Q residue 13 PHE Chi-restraints excluded: chain Q residue 117 ARG Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 127 TRP Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 142 ARG Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 56 CYS Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 207 VAL Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 285 CYS Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 61 ARG Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 549 VAL Chi-restraints excluded: chain u residue 560 LEU Chi-restraints excluded: chain u residue 591 MET Chi-restraints excluded: chain u residue 636 ASP Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 745 LEU Chi-restraints excluded: chain w residue 232 GLN Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 250 MET Chi-restraints excluded: chain t residue 251 ARG Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 349 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 379 optimal weight: 9.9990 chunk 492 optimal weight: 5.9990 chunk 660 optimal weight: 9.9990 chunk 189 optimal weight: 30.0000 chunk 571 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 620 optimal weight: 0.6980 chunk 259 optimal weight: 0.9980 chunk 637 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 ASN S 125 HIS ** T 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS C 235 ASN E 67 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN H 165 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 ASN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 HIS L 19 ASN ** u 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 256 HIS ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 408 GLN ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.156238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.132464 restraints weight = 123451.010| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.62 r_work: 0.3451 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.313 90101 Z= 0.302 Angle : 0.663 59.199 129421 Z= 0.342 Chirality : 0.039 0.369 15871 Planarity : 0.005 0.077 10386 Dihedral : 22.553 179.184 32311 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.12 % Rotamer: Outliers : 1.89 % Allowed : 21.63 % Favored : 76.48 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.02 % 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 (0.11), residues: 6239 helix: 1.46 (0.10), residues: 2683 sheet: -0.11 (0.17), residues: 872 loop : -0.87 (0.12), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP w 213 HIS 0.007 0.001 HIS u 144 PHE 0.027 0.002 PHE w 204 TYR 0.019 0.001 TYR K 720 ARG 0.025 0.001 ARG Q 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23825.07 seconds wall clock time: 418 minutes 0.83 seconds (25080.83 seconds total)