Starting phenix.real_space_refine on Sun Sep 29 16:08:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eml_3886/09_2024/6eml_3886.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eml_3886/09_2024/6eml_3886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eml_3886/09_2024/6eml_3886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eml_3886/09_2024/6eml_3886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eml_3886/09_2024/6eml_3886.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eml_3886/09_2024/6eml_3886.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 1675 5.49 5 S 92 5.16 5 C 41271 2.51 5 N 13814 2.21 5 O 19034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 75886 Number of models: 1 Model: "" Number of chains: 32 Chain: "2" Number of atoms: 35695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1675, 35695 Classifications: {'RNA': 1675} Modifications used: {'rna2p_pur': 104, 'rna2p_pyr': 89, 'rna3p_pur': 779, 'rna3p_pyr': 703} Link IDs: {'rna2p': 193, 'rna3p': 1481} Chain breaks: 10 Chain: "D" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 892 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1592 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 871 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 928 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "F" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 134} Chain: "H" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1009 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "K" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 519 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "L" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 486 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "N" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 397 Classifications: {'peptide': 51} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 48} Chain: "P" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1577 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 189} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "Q" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1709 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "R" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1662 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 13, 'TRANS': 206} Chain: "S" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "T" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1799 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 216} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1481 Classifications: {'peptide': 184} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 172} Chain: "V" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "W" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "X" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1213 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 146} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "Y" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "Z" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 891 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "a" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 684 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "b" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "c" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "d" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "f" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "t" Number of atoms: 5037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5037 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 31, 'TRANS': 601} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "g" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 475 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain: "p" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1473 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "r" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 253} Chain breaks: 3 Chain: "e" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1045 Classifications: {'peptide': 261} Incomplete info: {'backbone_only': 250, 'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 14, 'TRANS': 244} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1133 Unresolved non-hydrogen angles: 1638 Unresolved non-hydrogen dihedrals: 750 Unresolved non-hydrogen chiralities: 333 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 13, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 14, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 529 Time building chain proxies: 31.60, per 1000 atoms: 0.42 Number of scatterers: 75886 At special positions: 0 Unit cell: (226.556, 241.732, 198.372, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 1675 15.00 O 19034 8.00 N 13814 7.00 C 41271 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 - 3.00 Amino acid : True - 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: 13.68 Conformation dependent library (CDL) restraints added in 4.8 seconds 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9282 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 47 sheets defined 34.6% alpha, 12.1% beta 458 base pairs and 814 stacking pairs defined. Time for finding SS restraints: 25.13 Creating SS restraints... Processing helix chain 'D' and resid 26 through 35 removed outlier: 3.712A pdb=" N VAL D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 79 removed outlier: 3.583A pdb=" N GLY D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 107 through 111 removed outlier: 4.113A pdb=" N ASN D 111 " --> pdb=" O ARG D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 137 removed outlier: 4.322A pdb=" N ILE D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.641A pdb=" N GLN B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 removed outlier: 3.636A pdb=" N LEU B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.752A pdb=" N ASN B 103 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.978A pdb=" N ALA B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 141 removed outlier: 4.181A pdb=" N VAL B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 182 removed outlier: 3.901A pdb=" N ALA B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 208 through 225 removed outlier: 3.778A pdb=" N LYS B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 removed outlier: 3.941A pdb=" N ALA C 15 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE C 17 " --> pdb=" O SER C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.964A pdb=" N ILE C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'E' and resid 21 through 27 Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 56 through 65 removed outlier: 3.514A pdb=" N LYS E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 112 removed outlier: 4.020A pdb=" N LEU E 112 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.694A pdb=" N PHE E 119 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 54 Proline residue: F 51 - end of helix Processing helix chain 'F' and resid 73 through 88 removed outlier: 3.579A pdb=" N GLN F 77 " --> pdb=" O GLY F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 111 removed outlier: 4.011A pdb=" N ASN F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 33 removed outlier: 4.169A pdb=" N LEU H 32 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 33' Processing helix chain 'H' and resid 39 through 50 Processing helix chain 'H' and resid 62 through 75 removed outlier: 3.577A pdb=" N ILE H 69 " --> pdb=" O GLU H 65 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN H 75 " --> pdb=" O GLN H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 118 removed outlier: 3.708A pdb=" N SER H 107 " --> pdb=" O ASN H 103 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU H 114 " --> pdb=" O ARG H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 130 Processing helix chain 'I' and resid 10 through 25 removed outlier: 3.799A pdb=" N PHE I 14 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA I 19 " --> pdb=" O ILE I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 67 removed outlier: 3.890A pdb=" N ARG I 57 " --> pdb=" O TRP I 53 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA I 58 " --> pdb=" O PHE I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 81 removed outlier: 3.615A pdb=" N LEU I 76 " --> pdb=" O GLY I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 105 through 111 removed outlier: 3.969A pdb=" N GLU I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 143 removed outlier: 4.036A pdb=" N GLN I 138 " --> pdb=" O ARG I 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 54 removed outlier: 3.618A pdb=" N LYS K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'P' and resid 10 through 20 removed outlier: 3.810A pdb=" N LEU P 16 " --> pdb=" O GLU P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 67 removed outlier: 3.579A pdb=" N LEU P 59 " --> pdb=" O GLU P 55 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 Processing helix chain 'P' and resid 129 through 138 removed outlier: 3.603A pdb=" N ILE P 133 " --> pdb=" O ASP P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 184 Processing helix chain 'Q' and resid 57 through 61 Processing helix chain 'Q' and resid 70 through 74 Processing helix chain 'Q' and resid 106 through 114 Processing helix chain 'Q' and resid 159 through 175 Processing helix chain 'Q' and resid 181 through 189 Processing helix chain 'Q' and resid 191 through 202 removed outlier: 4.138A pdb=" N LYS Q 195 " --> pdb=" O GLU Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 231 Processing helix chain 'R' and resid 40 through 48 removed outlier: 3.505A pdb=" N LEU R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 58 Processing helix chain 'R' and resid 66 through 73 removed outlier: 3.561A pdb=" N ASP R 70 " --> pdb=" O PHE R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 135 Processing helix chain 'R' and resid 181 through 190 removed outlier: 3.535A pdb=" N LEU R 190 " --> pdb=" O LYS R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 220 Processing helix chain 'R' and resid 221 through 223 No H-bonds generated for 'chain 'R' and resid 221 through 223' Processing helix chain 'R' and resid 226 through 231 removed outlier: 3.608A pdb=" N TRP R 230 " --> pdb=" O PRO R 227 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA R 231 " --> pdb=" O ASN R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 246 removed outlier: 4.688A pdb=" N ASP R 245 " --> pdb=" O ILE R 242 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 19 Processing helix chain 'S' and resid 44 through 50 Processing helix chain 'S' and resid 57 through 66 Processing helix chain 'S' and resid 117 through 121 removed outlier: 3.700A pdb=" N TYR S 121 " --> pdb=" O GLU S 118 " (cutoff:3.500A) Processing helix chain 'S' and resid 133 through 135 No H-bonds generated for 'chain 'S' and resid 133 through 135' Processing helix chain 'S' and resid 250 through 258 removed outlier: 4.277A pdb=" N ARG S 256 " --> pdb=" O ARG S 252 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 27 removed outlier: 3.986A pdb=" N VAL T 26 " --> pdb=" O ARG T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 61 removed outlier: 4.107A pdb=" N PHE T 61 " --> pdb=" O LYS T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 137 through 146 Processing helix chain 'T' and resid 180 through 221 removed outlier: 3.896A pdb=" N LEU T 184 " --> pdb=" O THR T 180 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS T 194 " --> pdb=" O GLN T 190 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL T 195 " --> pdb=" O ARG T 191 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU T 207 " --> pdb=" O GLU T 203 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER T 217 " --> pdb=" O ALA T 213 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 27 Processing helix chain 'U' and resid 66 through 72 removed outlier: 3.679A pdb=" N PHE U 70 " --> pdb=" O SER U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 85 Processing helix chain 'U' and resid 113 through 116 Processing helix chain 'U' and resid 117 through 130 removed outlier: 3.595A pdb=" N ASP U 128 " --> pdb=" O LYS U 124 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL U 130 " --> pdb=" O LEU U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 165 through 177 removed outlier: 3.830A pdb=" N GLN U 170 " --> pdb=" O LEU U 166 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA U 171 " --> pdb=" O GLU U 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 10 removed outlier: 3.958A pdb=" N HIS V 9 " --> pdb=" O ASP V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 116 Processing helix chain 'V' and resid 136 through 146 removed outlier: 3.631A pdb=" N ARG V 146 " --> pdb=" O LYS V 142 " (cutoff:3.500A) Processing helix chain 'V' and resid 153 through 161 removed outlier: 4.331A pdb=" N GLN V 159 " --> pdb=" O SER V 155 " (cutoff:3.500A) Processing helix chain 'V' and resid 172 through 177 Processing helix chain 'V' and resid 185 through 197 removed outlier: 3.562A pdb=" N LEU V 189 " --> pdb=" O GLU V 185 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 35 removed outlier: 3.549A pdb=" N ASP W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU W 28 " --> pdb=" O LEU W 24 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS W 29 " --> pdb=" O ASP W 25 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 60 removed outlier: 4.247A pdb=" N ILE W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU W 59 " --> pdb=" O ALA W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 83 removed outlier: 3.754A pdb=" N VAL W 83 " --> pdb=" O ARG W 79 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 105 removed outlier: 3.880A pdb=" N PHE W 104 " --> pdb=" O LYS W 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 117 removed outlier: 3.833A pdb=" N TYR W 114 " --> pdb=" O GLN W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 123 through 131 Processing helix chain 'W' and resid 151 through 155 removed outlier: 3.806A pdb=" N LYS W 154 " --> pdb=" O ASP W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 171 through 178 Processing helix chain 'X' and resid 45 through 51 removed outlier: 3.626A pdb=" N ILE X 49 " --> pdb=" O PRO X 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.547A pdb=" N VAL Y 33 " --> pdb=" O SER Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 57 Processing helix chain 'Y' and resid 62 through 67 removed outlier: 3.645A pdb=" N ILE Y 66 " --> pdb=" O GLN Y 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 70 through 78 Processing helix chain 'Y' and resid 85 through 105 Processing helix chain 'Y' and resid 109 through 133 removed outlier: 4.054A pdb=" N THR Y 131 " --> pdb=" O ARG Y 127 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL Y 132 " --> pdb=" O TYR Y 128 " (cutoff:3.500A) Processing helix chain 'Y' and resid 145 through 150 Processing helix chain 'Z' and resid 43 through 47 removed outlier: 3.650A pdb=" N MET Z 46 " --> pdb=" O THR Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 55 removed outlier: 3.676A pdb=" N SER Z 55 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 52 through 55' Processing helix chain 'Z' and resid 56 through 75 removed outlier: 3.871A pdb=" N LEU Z 62 " --> pdb=" O TYR Z 58 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN Z 65 " --> pdb=" O MET Z 61 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP Z 66 " --> pdb=" O LEU Z 62 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS Z 70 " --> pdb=" O ASP Z 66 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS Z 71 " --> pdb=" O VAL Z 67 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS Z 72 " --> pdb=" O ALA Z 68 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU Z 73 " --> pdb=" O ALA Z 69 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 106 Processing helix chain 'a' and resid 56 through 63 removed outlier: 3.549A pdb=" N ARG a 60 " --> pdb=" O SER a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 64 through 75 Processing helix chain 'b' and resid 5 through 20 removed outlier: 3.780A pdb=" N THR b 20 " --> pdb=" O ASN b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 44 removed outlier: 3.612A pdb=" N HIS b 44 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 84 No H-bonds generated for 'chain 'b' and resid 82 through 84' Processing helix chain 'b' and resid 85 through 90 Processing helix chain 'b' and resid 113 through 117 Processing helix chain 'c' and resid 11 through 23 removed outlier: 3.633A pdb=" N LEU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 34 removed outlier: 3.517A pdb=" N LEU c 33 " --> pdb=" O TYR c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 39 Processing helix chain 'c' and resid 131 through 137 removed outlier: 3.538A pdb=" N LEU c 135 " --> pdb=" O SER c 131 " (cutoff:3.500A) Processing helix chain 'd' and resid 36 through 49 removed outlier: 3.767A pdb=" N LEU d 40 " --> pdb=" O SER d 36 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA d 45 " --> pdb=" O ARG d 41 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL d 47 " --> pdb=" O LYS d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 53 No H-bonds generated for 'chain 'd' and resid 51 through 53' Processing helix chain 'd' and resid 78 through 84 Processing helix chain 'd' and resid 87 through 94 Processing helix chain 'd' and resid 104 through 114 Processing helix chain 'd' and resid 122 through 133 removed outlier: 3.514A pdb=" N ALA d 126 " --> pdb=" O GLY d 122 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA d 130 " --> pdb=" O ALA d 126 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG d 131 " --> pdb=" O LYS d 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 17 removed outlier: 4.116A pdb=" N ARG f 17 " --> pdb=" O ALA f 13 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 58 Processing helix chain 't' and resid 59 through 73 removed outlier: 3.503A pdb=" N ARG t 65 " --> pdb=" O LEU t 61 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG t 73 " --> pdb=" O SER t 69 " (cutoff:3.500A) Processing helix chain 't' and resid 97 through 105 removed outlier: 3.541A pdb=" N LEU t 101 " --> pdb=" O PRO t 97 " (cutoff:3.500A) Processing helix chain 't' and resid 106 through 109 removed outlier: 3.764A pdb=" N ASP t 109 " --> pdb=" O LYS t 106 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 106 through 109' Processing helix chain 't' and resid 144 through 152 Processing helix chain 't' and resid 172 through 184 Processing helix chain 't' and resid 195 through 200 Processing helix chain 't' and resid 207 through 218 removed outlier: 3.945A pdb=" N HIS t 218 " --> pdb=" O SER t 214 " (cutoff:3.500A) Processing helix chain 't' and resid 231 through 245 removed outlier: 3.671A pdb=" N ARG t 245 " --> pdb=" O THR t 241 " (cutoff:3.500A) Processing helix chain 't' and resid 250 through 255 Processing helix chain 't' and resid 463 through 482 removed outlier: 3.654A pdb=" N GLU t 481 " --> pdb=" O LYS t 477 " (cutoff:3.500A) Processing helix chain 't' and resid 522 through 526 removed outlier: 4.159A pdb=" N LYS t 526 " --> pdb=" O ALA t 523 " (cutoff:3.500A) Processing helix chain 't' and resid 534 through 548 removed outlier: 4.720A pdb=" N ARG t 540 " --> pdb=" O ASN t 536 " (cutoff:3.500A) Processing helix chain 't' and resid 567 through 571 removed outlier: 3.658A pdb=" N LYS t 570 " --> pdb=" O LEU t 567 " (cutoff:3.500A) Processing helix chain 't' and resid 724 through 731 removed outlier: 4.306A pdb=" N GLU t 728 " --> pdb=" O PRO t 724 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TRP t 729 " --> pdb=" O GLU t 725 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE t 730 " --> pdb=" O ASP t 726 " (cutoff:3.500A) Processing helix chain 'g' and resid 5 through 9 removed outlier: 3.595A pdb=" N ALA g 9 " --> pdb=" O GLY g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 33 No H-bonds generated for 'chain 'g' and resid 31 through 33' Processing helix chain 'g' and resid 34 through 44 removed outlier: 3.503A pdb=" N ARG g 42 " --> pdb=" O LEU g 38 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 112 Proline residue: p 108 - end of helix Processing helix chain 'p' and resid 116 through 124 removed outlier: 3.851A pdb=" N LEU p 124 " --> pdb=" O LEU p 120 " (cutoff:3.500A) Processing helix chain 'p' and resid 150 through 165 removed outlier: 3.852A pdb=" N GLY p 165 " --> pdb=" O ALA p 161 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 173 removed outlier: 3.522A pdb=" N ALA p 173 " --> pdb=" O ASP p 169 " (cutoff:3.500A) Processing helix chain 'p' and resid 196 through 207 removed outlier: 3.672A pdb=" N ILE p 202 " --> pdb=" O LEU p 198 " (cutoff:3.500A) Processing helix chain 'p' and resid 210 through 219 Processing helix chain 'p' and resid 237 through 252 Processing helix chain 'p' and resid 255 through 272 removed outlier: 3.739A pdb=" N VAL p 259 " --> pdb=" O PRO p 255 " (cutoff:3.500A) Processing helix chain 'r' and resid 12 through 29 removed outlier: 3.911A pdb=" N PHE r 16 " --> pdb=" O THR r 12 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG r 17 " --> pdb=" O THR r 13 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG r 27 " --> pdb=" O GLU r 23 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER r 28 " --> pdb=" O GLN r 24 " (cutoff:3.500A) Processing helix chain 'r' and resid 34 through 39 removed outlier: 4.026A pdb=" N HIS r 38 " --> pdb=" O THR r 34 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN r 39 " --> pdb=" O PRO r 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 34 through 39' Processing helix chain 'r' and resid 47 through 59 removed outlier: 3.619A pdb=" N ARG r 51 " --> pdb=" O SER r 47 " (cutoff:3.500A) Processing helix chain 'r' and resid 76 through 92 removed outlier: 3.825A pdb=" N ASP r 81 " --> pdb=" O TYR r 77 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR r 82 " --> pdb=" O ASN r 78 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP r 92 " --> pdb=" O MET r 88 " (cutoff:3.500A) Processing helix chain 'r' and resid 152 through 171 removed outlier: 3.755A pdb=" N ALA r 159 " --> pdb=" O SER r 155 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN r 160 " --> pdb=" O ARG r 156 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE r 165 " --> pdb=" O LYS r 161 " (cutoff:3.500A) Processing helix chain 'r' and resid 206 through 221 removed outlier: 3.826A pdb=" N VAL r 218 " --> pdb=" O MET r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 264 through 283 removed outlier: 3.912A pdb=" N TYR r 268 " --> pdb=" O ASP r 264 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN r 270 " --> pdb=" O ASP r 266 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG r 271 " --> pdb=" O TYR r 267 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE r 280 " --> pdb=" O ILE r 276 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS r 281 " --> pdb=" O ARG r 277 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS r 282 " --> pdb=" O ARG r 278 " (cutoff:3.500A) Processing helix chain 'e' and resid 213 through 222 removed outlier: 3.525A pdb=" N LYS e 222 " --> pdb=" O GLY e 218 " (cutoff:3.500A) Processing helix chain 'e' and resid 232 through 236 removed outlier: 3.809A pdb=" N VAL e 235 " --> pdb=" O LEU e 232 " (cutoff:3.500A) Processing helix chain 'e' and resid 241 through 247 removed outlier: 3.527A pdb=" N TYR e 247 " --> pdb=" O GLN e 243 " (cutoff:3.500A) Processing helix chain 'e' and resid 250 through 254 removed outlier: 3.864A pdb=" N TRP e 254 " --> pdb=" O PRO e 251 " (cutoff:3.500A) Processing helix chain 'e' and resid 255 through 268 removed outlier: 3.582A pdb=" N SER e 268 " --> pdb=" O LYS e 264 " (cutoff:3.500A) Processing helix chain 'e' and resid 271 through 282 Processing helix chain 'e' and resid 282 through 293 Processing helix chain 'e' and resid 305 through 310 Processing helix chain 'e' and resid 313 through 321 removed outlier: 3.910A pdb=" N PHE e 317 " --> pdb=" O LYS e 313 " (cutoff:3.500A) Processing helix chain 'e' and resid 321 through 328 removed outlier: 3.694A pdb=" N GLU e 327 " --> pdb=" O PHE e 323 " (cutoff:3.500A) Processing helix chain 'e' and resid 331 through 344 removed outlier: 3.982A pdb=" N ALA e 343 " --> pdb=" O GLY e 339 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS e 344 " --> pdb=" O SER e 340 " (cutoff:3.500A) Processing helix chain 'e' and resid 348 through 361 Processing helix chain 'e' and resid 365 through 377 removed outlier: 3.594A pdb=" N PHE e 371 " --> pdb=" O PRO e 367 " (cutoff:3.500A) Processing helix chain 'e' and resid 383 through 396 removed outlier: 4.218A pdb=" N ARG e 396 " --> pdb=" O TYR e 392 " (cutoff:3.500A) Processing helix chain 'e' and resid 414 through 428 removed outlier: 3.906A pdb=" N HIS e 418 " --> pdb=" O PRO e 414 " (cutoff:3.500A) Processing helix chain 'e' and resid 433 through 448 removed outlier: 3.624A pdb=" N GLN e 446 " --> pdb=" O GLU e 442 " (cutoff:3.500A) Processing helix chain 'e' and resid 452 through 462 Processing sheet with id=AA1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AA2, first strand: chain 'E' and resid 76 through 78 removed outlier: 5.807A pdb=" N VAL E 76 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR E 97 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N THR E 78 " --> pdb=" O TYR E 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 8 through 13 removed outlier: 3.600A pdb=" N VAL F 67 " --> pdb=" O LYS F 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 15 through 17 removed outlier: 3.538A pdb=" N LEU H 17 " --> pdb=" O THR H 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 82 through 84 removed outlier: 3.629A pdb=" N GLY I 82 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE I 94 " --> pdb=" O GLY I 82 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS I 92 " --> pdb=" O LYS I 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 114 through 115 Processing sheet with id=AA7, first strand: chain 'K' and resid 89 through 91 removed outlier: 3.877A pdb=" N LYS K 90 " --> pdb=" O ARG K 103 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG K 103 " --> pdb=" O LYS K 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 15 through 18 removed outlier: 6.184A pdb=" N GLN L 27 " --> pdb=" O LEU L 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 37 through 38 removed outlier: 3.934A pdb=" N VAL P 47 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 98 through 99 removed outlier: 6.176A pdb=" N VAL P 121 " --> pdb=" O ILE P 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 42 through 47 removed outlier: 3.745A pdb=" N LEU Q 96 " --> pdb=" O ASP Q 31 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LYS Q 85 " --> pdb=" O HIS Q 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N MET Q 103 " --> pdb=" O LYS Q 83 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS Q 83 " --> pdb=" O MET Q 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 121 through 128 removed outlier: 3.719A pdb=" N ALA Q 123 " --> pdb=" O ALA Q 139 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL Q 125 " --> pdb=" O ILE Q 137 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE Q 137 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL Q 134 " --> pdb=" O LEU Q 218 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU Q 218 " --> pdb=" O VAL Q 134 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS Q 214 " --> pdb=" O PHE Q 138 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE Q 140 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL Q 212 " --> pdb=" O ILE Q 140 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE Q 142 " --> pdb=" O ILE Q 210 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE Q 210 " --> pdb=" O PHE Q 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 79 through 84 removed outlier: 6.773A pdb=" N VAL R 101 " --> pdb=" O MET R 81 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE R 83 " --> pdb=" O LYS R 99 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS R 99 " --> pdb=" O ILE R 83 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS R 110 " --> pdb=" O ASP R 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 158 through 162 Processing sheet with id=AB6, first strand: chain 'S' and resid 42 through 43 Processing sheet with id=AB7, first strand: chain 'S' and resid 70 through 72 removed outlier: 4.285A pdb=" N ASN S 98 " --> pdb=" O ILE S 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.741A pdb=" N TYR S 138 " --> pdb=" O VAL S 129 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL S 129 " --> pdb=" O TYR S 138 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL S 140 " --> pdb=" O LYS S 127 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP S 171 " --> pdb=" O LYS S 161 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 180 through 183 removed outlier: 6.318A pdb=" N LEU S 180 " --> pdb=" O ILE S 228 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 207 through 211 Processing sheet with id=AC2, first strand: chain 'T' and resid 12 through 17 removed outlier: 3.509A pdb=" N SER T 12 " --> pdb=" O TYR T 7 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU T 111 " --> pdb=" O LYS T 2 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASN T 4 " --> pdb=" O LEU T 111 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE T 113 " --> pdb=" O ASN T 4 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER T 6 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA T 110 " --> pdb=" O SER T 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 72 through 77 removed outlier: 3.783A pdb=" N LYS T 93 " --> pdb=" O LEU T 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 161 through 163 Processing sheet with id=AC5, first strand: chain 'U' and resid 46 through 50 removed outlier: 3.660A pdb=" N VAL U 62 " --> pdb=" O LEU U 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 181 through 184 removed outlier: 8.385A pdb=" N VAL U 182 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN U 150 " --> pdb=" O VAL U 182 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLU U 184 " --> pdb=" O GLN U 150 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL U 152 " --> pdb=" O GLU U 184 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE U 149 " --> pdb=" O ARG U 141 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY U 137 " --> pdb=" O LEU U 153 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS U 138 " --> pdb=" O ASP b 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE b 50 " --> pdb=" O TYR U 142 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 42 through 48 removed outlier: 3.741A pdb=" N ARG V 56 " --> pdb=" O HIS V 44 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR V 48 " --> pdb=" O ASN V 52 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASN V 52 " --> pdb=" O THR V 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'V' and resid 62 through 63 removed outlier: 6.403A pdb=" N GLN V 103 " --> pdb=" O ALA V 79 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL V 81 " --> pdb=" O ILE V 101 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE V 101 " --> pdb=" O VAL V 81 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 134 through 135 Processing sheet with id=AD1, first strand: chain 'X' and resid 67 through 76 removed outlier: 26.786A pdb=" N GLY X 68 " --> pdb=" O TYR X 93 " (cutoff:3.500A) removed outlier: 23.041A pdb=" N TYR X 93 " --> pdb=" O GLY X 68 " (cutoff:3.500A) removed outlier: 17.686A pdb=" N ILE X 70 " --> pdb=" O LEU X 91 " (cutoff:3.500A) removed outlier: 15.123A pdb=" N LEU X 91 " --> pdb=" O ILE X 70 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N THR X 72 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA X 89 " --> pdb=" O THR X 72 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR X 74 " --> pdb=" O ARG X 87 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL X 85 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG X 99 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N PHE X 137 " --> pdb=" O ASN X 106 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL X 139 " --> pdb=" O PRO X 108 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N HIS X 110 " --> pdb=" O VAL X 139 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LYS X 141 " --> pdb=" O HIS X 110 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR X 124 " --> pdb=" O VAL X 140 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL X 142 " --> pdb=" O ILE X 122 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE X 122 " --> pdb=" O VAL X 142 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS X 69 " --> pdb=" O GLN X 127 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Z' and resid 20 through 21 Processing sheet with id=AD3, first strand: chain 'Z' and resid 30 through 31 Processing sheet with id=AD4, first strand: chain 'Z' and resid 82 through 83 Processing sheet with id=AD5, first strand: chain 'a' and resid 15 through 16 removed outlier: 4.425A pdb=" N ARG a 15 " --> pdb=" O ILE a 24 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'a' and resid 32 through 37 Processing sheet with id=AD7, first strand: chain 'b' and resid 71 through 72 removed outlier: 4.987A pdb=" N ILE b 125 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR b 105 " --> pdb=" O ILE b 125 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY b 127 " --> pdb=" O ILE b 103 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'c' and resid 48 through 56 removed outlier: 6.611A pdb=" N ARG c 73 " --> pdb=" O LEU c 54 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYS c 56 " --> pdb=" O CYS c 71 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N CYS c 71 " --> pdb=" O LYS c 56 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE c 122 " --> pdb=" O THR c 84 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU c 103 " --> pdb=" O VAL c 125 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL c 127 " --> pdb=" O GLU c 101 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU c 101 " --> pdb=" O VAL c 127 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 7 through 15 removed outlier: 4.291A pdb=" N VAL d 12 " --> pdb=" O GLN d 22 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN d 22 " --> pdb=" O VAL d 12 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER d 14 " --> pdb=" O ARG d 20 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG d 20 " --> pdb=" O SER d 14 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS d 68 " --> pdb=" O THR d 62 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N THR d 62 " --> pdb=" O LYS d 68 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL d 70 " --> pdb=" O PHE d 60 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'f' and resid 44 through 47 Processing sheet with id=AE2, first strand: chain 'f' and resid 55 through 56 removed outlier: 3.617A pdb=" N THR f 61 " --> pdb=" O CYS f 56 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 't' and resid 123 through 128 removed outlier: 6.511A pdb=" N LYS t 84 " --> pdb=" O LYS t 136 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE t 138 " --> pdb=" O LYS t 84 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE t 86 " --> pdb=" O ILE t 138 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE t 85 " --> pdb=" O PHE t 157 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL t 159 " --> pdb=" O ILE t 85 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR t 87 " --> pdb=" O VAL t 159 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLY t 161 " --> pdb=" O THR t 87 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL t 89 " --> pdb=" O GLY t 161 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 't' and resid 337 through 338 removed outlier: 4.490A pdb=" N GLN t 302 " --> pdb=" O ARG t 562 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE t 560 " --> pdb=" O ASN t 304 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE t 306 " --> pdb=" O ARG t 558 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG t 558 " --> pdb=" O ILE t 306 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LYS t 308 " --> pdb=" O ARG t 556 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG t 556 " --> pdb=" O LYS t 308 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE t 561 " --> pdb=" O LEU t 276 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP t 275 " --> pdb=" O PHE t 266 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N PHE t 266 " --> pdb=" O ASP t 275 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL t 277 " --> pdb=" O VAL t 264 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL t 264 " --> pdb=" O VAL t 277 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU t 279 " --> pdb=" O ASP t 262 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR t 281 " --> pdb=" O VAL t 260 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL t 260 " --> pdb=" O THR t 281 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 't' and resid 591 through 595 removed outlier: 3.546A pdb=" N CYS t 656 " --> pdb=" O VAL t 594 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 't' and resid 598 through 600 removed outlier: 4.991A pdb=" N LEU t 682 " --> pdb=" O LYS t 671 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS t 671 " --> pdb=" O LEU t 682 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU t 783 " --> pdb=" O THR t 624 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 't' and resid 639 through 641 removed outlier: 6.639A pdb=" N HIS t 640 " --> pdb=" O ALA t 698 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ARG t 700 " --> pdb=" O HIS t 640 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 't' and resid 703 through 705 Processing sheet with id=AE9, first strand: chain 'p' and resid 97 through 100 removed outlier: 4.233A pdb=" N ARG p 97 " --> pdb=" O LEU p 139 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU p 139 " --> pdb=" O ARG p 97 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'p' and resid 181 through 183 Processing sheet with id=AF2, first strand: chain 'r' and resid 96 through 103 removed outlier: 3.655A pdb=" N SER r 96 " --> pdb=" O SER r 113 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS r 111 " --> pdb=" O GLY r 98 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR r 100 " --> pdb=" O ILE r 109 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE r 109 " --> pdb=" O THR r 100 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLY r 102 " --> pdb=" O SER r 107 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N SER r 107 " --> pdb=" O GLY r 102 " (cutoff:3.500A) 1334 hydrogen bonds defined for protein. 3780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1111 hydrogen bonds 1814 hydrogen bond angles 0 basepair planarities 458 basepair parallelities 814 stacking parallelities Total time for adding SS restraints: 56.12 Time building geometry restraints manager: 16.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.19: 115 1.19 - 1.35: 21542 1.35 - 1.52: 42009 1.52 - 1.68: 16969 1.68 - 1.85: 152 Bond restraints: 80787 Sorted by residual: bond pdb=" C6 A 2 220 " pdb=" N1 A 2 220 " ideal model delta sigma weight residual 1.351 1.024 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C6 A 2 222 " pdb=" N1 A 2 222 " ideal model delta sigma weight residual 1.351 1.044 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C1' C 21235 " pdb=" N1 C 21235 " ideal model delta sigma weight residual 1.480 1.682 -0.202 1.50e-02 4.44e+03 1.81e+02 bond pdb=" C2 U 2 831 " pdb=" N3 U 2 831 " ideal model delta sigma weight residual 1.373 1.611 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C2 U 2 833 " pdb=" N3 U 2 833 " ideal model delta sigma weight residual 1.373 1.601 -0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 80782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 113736 3.97 - 7.94: 3106 7.94 - 11.91: 241 11.91 - 15.88: 29 15.88 - 19.85: 6 Bond angle restraints: 117118 Sorted by residual: angle pdb=" C4' A 21023 " pdb=" C3' A 21023 " pdb=" O3' A 21023 " ideal model delta sigma weight residual 109.40 123.21 -13.81 1.50e+00 4.44e-01 8.47e+01 angle pdb=" O2' A 2 452 " pdb=" C2' A 2 452 " pdb=" C1' A 2 452 " ideal model delta sigma weight residual 111.80 98.34 13.46 1.50e+00 4.44e-01 8.05e+01 angle pdb=" C4' A 2 400 " pdb=" C3' A 2 400 " pdb=" O3' A 2 400 " ideal model delta sigma weight residual 109.40 122.60 -13.20 1.50e+00 4.44e-01 7.75e+01 angle pdb=" O3' G 2 322 " pdb=" C3' G 2 322 " pdb=" C2' G 2 322 " ideal model delta sigma weight residual 109.50 121.85 -12.35 1.50e+00 4.44e-01 6.78e+01 angle pdb=" CA GLY Y 10 " pdb=" C GLY Y 10 " pdb=" O GLY Y 10 " ideal model delta sigma weight residual 121.58 114.47 7.11 9.00e-01 1.23e+00 6.25e+01 ... (remaining 117113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 45604 35.87 - 71.75: 4442 71.75 - 107.62: 437 107.62 - 143.49: 27 143.49 - 179.37: 57 Dihedral angle restraints: 50567 sinusoidal: 35948 harmonic: 14619 Sorted by residual: dihedral pdb=" CA ALA Y 22 " pdb=" C ALA Y 22 " pdb=" N PRO Y 23 " pdb=" CA PRO Y 23 " ideal model delta harmonic sigma weight residual 180.00 110.51 69.49 0 5.00e+00 4.00e-02 1.93e+02 dihedral pdb=" CA ASP t 518 " pdb=" C ASP t 518 " pdb=" N PRO t 519 " pdb=" CA PRO t 519 " ideal model delta harmonic sigma weight residual -180.00 -111.34 -68.66 0 5.00e+00 4.00e-02 1.89e+02 dihedral pdb=" CA SER B 57 " pdb=" C SER B 57 " pdb=" N LEU B 58 " pdb=" CA LEU B 58 " ideal model delta harmonic sigma weight residual -180.00 -120.27 -59.73 0 5.00e+00 4.00e-02 1.43e+02 ... (remaining 50564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 13817 0.208 - 0.417: 560 0.417 - 0.625: 33 0.625 - 0.834: 3 0.834 - 1.042: 1 Chirality restraints: 14414 Sorted by residual: chirality pdb=" C3' A 2 400 " pdb=" C4' A 2 400 " pdb=" O3' A 2 400 " pdb=" C2' A 2 400 " both_signs ideal model delta sigma weight residual False -2.74 -1.70 -1.04 2.00e-01 2.50e+01 2.71e+01 chirality pdb=" C3' C 2 99 " pdb=" C4' C 2 99 " pdb=" O3' C 2 99 " pdb=" C2' C 2 99 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C3' U 2 609 " pdb=" C4' U 2 609 " pdb=" O3' U 2 609 " pdb=" C2' U 2 609 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 14411 not shown) Planarity restraints: 8812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 2 440 " -0.124 2.00e-02 2.50e+03 1.95e-01 8.59e+02 pdb=" N1 U 2 440 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U 2 440 " 0.029 2.00e-02 2.50e+03 pdb=" O2 U 2 440 " -0.125 2.00e-02 2.50e+03 pdb=" N3 U 2 440 " 0.412 2.00e-02 2.50e+03 pdb=" C4 U 2 440 " 0.155 2.00e-02 2.50e+03 pdb=" O4 U 2 440 " -0.333 2.00e-02 2.50e+03 pdb=" C5 U 2 440 " -0.069 2.00e-02 2.50e+03 pdb=" C6 U 2 440 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 857 " -0.075 2.00e-02 2.50e+03 1.22e-01 3.37e+02 pdb=" N1 U 2 857 " 0.001 2.00e-02 2.50e+03 pdb=" C2 U 2 857 " -0.016 2.00e-02 2.50e+03 pdb=" O2 U 2 857 " -0.060 2.00e-02 2.50e+03 pdb=" N3 U 2 857 " 0.255 2.00e-02 2.50e+03 pdb=" C4 U 2 857 " 0.106 2.00e-02 2.50e+03 pdb=" O4 U 2 857 " -0.209 2.00e-02 2.50e+03 pdb=" C5 U 2 857 " -0.051 2.00e-02 2.50e+03 pdb=" C6 U 2 857 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 618 " 0.014 2.00e-02 2.50e+03 1.21e-01 3.29e+02 pdb=" N1 U 2 618 " -0.023 2.00e-02 2.50e+03 pdb=" C2 U 2 618 " -0.036 2.00e-02 2.50e+03 pdb=" O2 U 2 618 " -0.128 2.00e-02 2.50e+03 pdb=" N3 U 2 618 " 0.311 2.00e-02 2.50e+03 pdb=" C4 U 2 618 " -0.052 2.00e-02 2.50e+03 pdb=" O4 U 2 618 " -0.114 2.00e-02 2.50e+03 pdb=" C5 U 2 618 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U 2 618 " 0.029 2.00e-02 2.50e+03 ... (remaining 8809 not shown) Histogram of nonbonded interaction distances: 0.38 - 1.29: 24 1.29 - 2.19: 130 2.19 - 3.09: 51310 3.09 - 4.00: 228672 4.00 - 4.90: 378401 Warning: very small nonbonded interaction distances. Nonbonded interactions: 658537 Sorted by model distance: nonbonded pdb=" O6 G 21149 " pdb=" CG GLN r 147 " model vdw 0.382 3.440 nonbonded pdb=" C4 C 2 565 " pdb=" O GLN r 46 " model vdw 0.496 3.260 nonbonded pdb=" N3 U 21269 " pdb=" O ASP e 296 " model vdw 0.660 3.120 nonbonded pdb=" C2 G 21149 " pdb=" N GLN r 147 " model vdw 0.669 3.340 nonbonded pdb=" N1 G 21149 " pdb=" CA GLN r 147 " model vdw 0.767 3.550 ... (remaining 658532 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 4.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 2.510 Check model and map are aligned: 0.460 Set scattering table: 0.570 Process input model: 169.970 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.250 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: 0.030 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.014 0.327 80787 Z= 0.901 Angle : 1.544 19.846 117118 Z= 0.890 Chirality : 0.101 1.042 14414 Planarity : 0.011 0.195 8812 Dihedral : 23.055 179.365 41285 Min Nonbonded Distance : 0.382 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 1.32 % Allowed : 12.50 % Favored : 86.18 % Rotamer: Outliers : 1.27 % Allowed : 4.48 % Favored : 94.24 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 2.25 % Twisted General : 0.80 % 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: -4.67 (0.09), residues: 5153 helix: -3.44 (0.08), residues: 1605 sheet: -2.45 (0.17), residues: 751 loop : -3.13 (0.10), residues: 2797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.010 TRP b 89 HIS 0.036 0.005 HIS S 8 PHE 0.055 0.008 PHE d 64 TYR 0.094 0.009 TYR g 40 ARG 0.094 0.004 ARG V 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1362 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1309 time to evaluate : 4.428 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: 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: B 49 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7183 (mm-30) REVERT: B 52 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6201 (mt-10) REVERT: B 54 LYS cc_start: 0.4647 (mtpp) cc_final: 0.4369 (mtpp) REVERT: B 58 LEU cc_start: 0.8198 (mt) cc_final: 0.7996 (tp) REVERT: B 81 ARG cc_start: 0.6506 (mtp85) cc_final: 0.6120 (ttt-90) REVERT: B 117 THR cc_start: 0.8206 (m) cc_final: 0.7858 (p) REVERT: B 148 ARG cc_start: 0.7433 (ttt180) cc_final: 0.7158 (ttm-80) REVERT: C 46 LEU cc_start: 0.4477 (tt) cc_final: 0.4213 (mp) REVERT: E 45 PHE cc_start: 0.7670 (m-80) cc_final: 0.7447 (t80) REVERT: E 77 ARG cc_start: 0.7953 (ptp90) cc_final: 0.7660 (pmt-80) REVERT: E 80 MET cc_start: 0.6283 (mtp) cc_final: 0.5891 (mtp) REVERT: E 87 PRO cc_start: 0.7748 (Cg_exo) cc_final: 0.7388 (Cg_endo) REVERT: E 97 TYR cc_start: 0.6318 (t80) cc_final: 0.5931 (t80) REVERT: F 116 LEU cc_start: 0.5983 (mp) cc_final: 0.5041 (tp) REVERT: H 56 LYS cc_start: 0.6285 (ttmt) cc_final: 0.5579 (mmtp) REVERT: H 99 HIS cc_start: 0.7559 (t70) cc_final: 0.7352 (t70) REVERT: I 127 ASN cc_start: 0.7383 (t0) cc_final: 0.7167 (t0) REVERT: I 131 ASP cc_start: 0.8753 (t70) cc_final: 0.8529 (t0) REVERT: L 27 GLN cc_start: 0.7513 (mt0) cc_final: 0.7162 (mp10) REVERT: L 57 MET cc_start: 0.5002 (ttm) cc_final: 0.4547 (tmm) REVERT: N 143 LYS cc_start: -0.0641 (OUTLIER) cc_final: -0.0961 (tptt) REVERT: P 7 PHE cc_start: 0.8318 (m-80) cc_final: 0.8102 (m-80) REVERT: P 8 ASP cc_start: 0.8978 (m-30) cc_final: 0.8401 (t70) REVERT: P 27 ARG cc_start: 0.7429 (tpp80) cc_final: 0.7112 (tpt90) REVERT: P 43 ASP cc_start: 0.7897 (m-30) cc_final: 0.7453 (t0) REVERT: P 117 GLU cc_start: 0.9061 (tt0) cc_final: 0.8513 (pm20) REVERT: P 119 ARG cc_start: 0.8624 (tpt170) cc_final: 0.8376 (mmm160) REVERT: P 123 VAL cc_start: 0.9082 (t) cc_final: 0.8561 (m) REVERT: P 125 ASP cc_start: 0.8665 (t0) cc_final: 0.8297 (t0) REVERT: P 128 SER cc_start: 0.8532 (m) cc_final: 0.8195 (p) REVERT: P 198 MET cc_start: 0.9208 (mmm) cc_final: 0.8944 (ttm) REVERT: Q 26 ARG cc_start: 0.8454 (ptp-170) cc_final: 0.8231 (mpp-170) REVERT: Q 62 LYS cc_start: 0.8354 (mttt) cc_final: 0.7740 (tmtt) REVERT: Q 79 HIS cc_start: 0.7840 (m90) cc_final: 0.7554 (m-70) REVERT: Q 117 TRP cc_start: 0.8655 (m100) cc_final: 0.8452 (m-90) REVERT: Q 122 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8044 (tt0) REVERT: Q 124 ASN cc_start: 0.8623 (p0) cc_final: 0.8300 (p0) REVERT: Q 132 ASP cc_start: 0.5983 (t0) cc_final: 0.5599 (t0) REVERT: Q 152 ARG cc_start: 0.8797 (ttt180) cc_final: 0.8486 (ttp-110) REVERT: Q 198 GLU cc_start: 0.8834 (tp30) cc_final: 0.8587 (tt0) REVERT: R 66 PHE cc_start: 0.9109 (p90) cc_final: 0.8733 (p90) REVERT: R 83 ILE cc_start: 0.8993 (mt) cc_final: 0.8716 (tt) REVERT: R 88 LYS cc_start: 0.7236 (pmmt) cc_final: 0.6794 (pttt) REVERT: R 90 THR cc_start: 0.5052 (OUTLIER) cc_final: 0.4621 (p) REVERT: R 119 LYS cc_start: 0.9343 (pmtt) cc_final: 0.8804 (ttmt) REVERT: R 120 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8492 (pt0) REVERT: R 176 SER cc_start: 0.9186 (m) cc_final: 0.8483 (t) REVERT: S 73 ASP cc_start: 0.8764 (m-30) cc_final: 0.8383 (m-30) REVERT: S 117 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8667 (tm-30) REVERT: S 118 GLU cc_start: 0.9097 (tt0) cc_final: 0.8854 (tm-30) REVERT: S 163 ASP cc_start: 0.8992 (t0) cc_final: 0.8644 (p0) REVERT: S 176 ASP cc_start: 0.8368 (t0) cc_final: 0.8127 (t0) REVERT: S 187 ARG cc_start: 0.8236 (tpt90) cc_final: 0.7995 (ttt90) REVERT: S 225 VAL cc_start: 0.9221 (t) cc_final: 0.8987 (p) REVERT: T 2 LYS cc_start: 0.7795 (ttmt) cc_final: 0.7592 (mptt) REVERT: T 29 ASP cc_start: 0.8960 (m-30) cc_final: 0.8578 (t0) REVERT: T 32 ILE cc_start: 0.9144 (mt) cc_final: 0.8924 (mp) REVERT: T 37 ASP cc_start: 0.8160 (m-30) cc_final: 0.7901 (m-30) REVERT: T 67 VAL cc_start: 0.9232 (m) cc_final: 0.8995 (t) REVERT: T 97 VAL cc_start: 0.8709 (t) cc_final: 0.8445 (m) REVERT: T 118 GLU cc_start: 0.7427 (pt0) cc_final: 0.6656 (mm-30) REVERT: T 150 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8337 (pp20) REVERT: T 151 ASP cc_start: 0.8031 (m-30) cc_final: 0.7045 (m-30) REVERT: T 190 GLN cc_start: 0.8865 (mm110) cc_final: 0.8469 (tm-30) REVERT: U 72 LYS cc_start: 0.7814 (mttt) cc_final: 0.7607 (mmmt) REVERT: U 95 GLU cc_start: 0.7416 (tp30) cc_final: 0.6699 (pp20) REVERT: U 148 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8577 (mttp) REVERT: U 164 TYR cc_start: 0.7909 (p90) cc_final: 0.7636 (p90) REVERT: U 167 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8815 (mm-30) REVERT: U 181 ILE cc_start: 0.8334 (mm) cc_final: 0.8085 (mm) REVERT: U 184 GLU cc_start: 0.8151 (tt0) cc_final: 0.7866 (tm-30) REVERT: V 46 VAL cc_start: 0.8686 (p) cc_final: 0.8451 (m) REVERT: V 59 ARG cc_start: 0.7058 (mtt180) cc_final: 0.6784 (mtm-85) REVERT: V 64 ASN cc_start: 0.8661 (t0) cc_final: 0.8432 (t0) REVERT: V 77 ARG cc_start: 0.8787 (ttp-170) cc_final: 0.8461 (ptm160) REVERT: V 179 CYS cc_start: 0.9309 (t) cc_final: 0.8979 (t) REVERT: W 54 ARG cc_start: 0.8682 (ttp80) cc_final: 0.8369 (ttm170) REVERT: W 64 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7840 (mm-30) REVERT: W 72 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8799 (tm-30) REVERT: X 11 ARG cc_start: 0.8052 (mtp85) cc_final: 0.7849 (mtp180) REVERT: X 25 VAL cc_start: 0.7444 (t) cc_final: 0.7131 (p) REVERT: X 46 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7946 (ttpp) REVERT: X 79 LYS cc_start: 0.9451 (mttp) cc_final: 0.9249 (mmmt) REVERT: X 82 ARG cc_start: 0.9153 (mtt180) cc_final: 0.8745 (mtp85) REVERT: X 116 ARG cc_start: 0.8878 (mtt90) cc_final: 0.8600 (tpt-90) REVERT: X 129 ARG cc_start: 0.8643 (ptt180) cc_final: 0.8398 (ptt180) REVERT: Y 33 VAL cc_start: 0.8445 (m) cc_final: 0.8073 (p) REVERT: Y 49 GLN cc_start: 0.8650 (mt0) cc_final: 0.8314 (mt0) REVERT: Y 64 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7509 (mmm160) REVERT: Y 80 LEU cc_start: 0.8249 (mp) cc_final: 0.8044 (tp) REVERT: Y 107 LYS cc_start: 0.8676 (tptp) cc_final: 0.8463 (mmmt) REVERT: Z 20 TYR cc_start: 0.7174 (t80) cc_final: 0.6548 (t80) REVERT: Z 41 ARG cc_start: 0.7692 (ttp-110) cc_final: 0.6622 (ttm-80) REVERT: Z 103 ARG cc_start: 0.7414 (mtp85) cc_final: 0.7188 (mtm-85) REVERT: Z 116 GLU cc_start: 0.7869 (pt0) cc_final: 0.7567 (pt0) REVERT: Z 123 SER cc_start: 0.8559 (m) cc_final: 0.8109 (p) REVERT: a 2 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8483 (mp0) REVERT: a 49 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8639 (mm-30) REVERT: a 85 TYR cc_start: 0.8288 (t80) cc_final: 0.7941 (t80) REVERT: b 24 GLN cc_start: 0.8696 (pm20) cc_final: 0.8476 (pm20) REVERT: b 88 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8087 (tttp) REVERT: c 26 GLU cc_start: 0.8428 (mp0) cc_final: 0.8197 (mt-10) REVERT: c 94 ASN cc_start: 0.7944 (m-40) cc_final: 0.7614 (p0) REVERT: c 99 ASN cc_start: 0.7841 (m-40) cc_final: 0.7513 (t0) REVERT: d 3 ASP cc_start: 0.5092 (t0) cc_final: 0.4439 (t70) REVERT: d 42 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8870 (tp30) REVERT: d 63 GLN cc_start: 0.8875 (tp40) cc_final: 0.8323 (tt0) REVERT: d 108 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.8117 (mtm110) REVERT: f 34 ASP cc_start: 0.7992 (m-30) cc_final: 0.7633 (p0) REVERT: f 45 THR cc_start: 0.8886 (m) cc_final: 0.8130 (p) REVERT: f 72 LYS cc_start: 0.7608 (tptt) cc_final: 0.7394 (ttpt) REVERT: f 79 PHE cc_start: 0.8347 (p90) cc_final: 0.8026 (p90) REVERT: f 80 ARG cc_start: 0.7728 (tpp-160) cc_final: 0.7334 (tpp80) REVERT: t 121 LYS cc_start: 0.6521 (mmtt) cc_final: 0.6163 (mttt) REVERT: t 132 LYS cc_start: 0.7849 (tttp) cc_final: 0.7580 (tppt) REVERT: t 171 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7570 (pp20) REVERT: t 175 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8482 (mm-40) REVERT: t 218 HIS cc_start: 0.7642 (m-70) cc_final: 0.7289 (t-90) REVERT: t 241 THR cc_start: 0.9353 (m) cc_final: 0.9108 (p) REVERT: t 342 ASN cc_start: 0.8033 (m-40) cc_final: 0.7645 (t0) REVERT: t 486 ILE cc_start: 0.7461 (tt) cc_final: 0.7257 (pt) REVERT: t 526 LYS cc_start: 0.7861 (mmtp) cc_final: 0.7656 (mmmt) REVERT: t 558 ARG cc_start: 0.7989 (mtt180) cc_final: 0.7654 (ttm110) REVERT: t 599 GLN cc_start: 0.8846 (tt0) cc_final: 0.8542 (mt0) REVERT: t 638 ASN cc_start: 0.8429 (t0) cc_final: 0.8188 (t0) REVERT: t 660 VAL cc_start: 0.8828 (t) cc_final: 0.8587 (p) REVERT: t 700 ARG cc_start: 0.7482 (ttt-90) cc_final: 0.7139 (ttp-170) REVERT: t 714 VAL cc_start: 0.6855 (OUTLIER) cc_final: 0.6621 (m) REVERT: t 754 TYR cc_start: 0.8002 (m-10) cc_final: 0.7241 (m-80) REVERT: g 31 LYS cc_start: 0.7621 (mtmm) cc_final: 0.7375 (mttm) REVERT: p 125 LYS cc_start: 0.8487 (mptt) cc_final: 0.8235 (mtmm) REVERT: p 126 LEU cc_start: 0.8263 (mp) cc_final: 0.7985 (mt) REVERT: p 129 ARG cc_start: 0.4729 (mtp-110) cc_final: 0.4076 (mmt180) REVERT: p 196 ASP cc_start: 0.8255 (m-30) cc_final: 0.7894 (t70) REVERT: p 220 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7889 (p) REVERT: p 231 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.7957 (mm) REVERT: p 264 ARG cc_start: 0.6293 (mmt90) cc_final: 0.6015 (ptt180) REVERT: p 269 ARG cc_start: 0.5839 (ptt180) cc_final: 0.5206 (ttp-170) REVERT: r 65 MET cc_start: 0.2935 (OUTLIER) cc_final: 0.1929 (ttp) REVERT: r 250 VAL cc_start: 0.4720 (t) cc_final: 0.4511 (t) outliers start: 53 outliers final: 11 residues processed: 1344 average time/residue: 0.8114 time to fit residues: 1781.4770 Evaluate side-chains 893 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 875 time to evaluate : 4.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 148 LYS Chi-restraints excluded: chain Z residue 137 LEU Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain t residue 303 LEU Chi-restraints excluded: chain t residue 714 VAL Chi-restraints excluded: chain p residue 164 LEU Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain p residue 220 THR Chi-restraints excluded: chain p residue 231 ILE Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain r residue 235 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 573 optimal weight: 8.9990 chunk 514 optimal weight: 0.9980 chunk 285 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 347 optimal weight: 0.8980 chunk 274 optimal weight: 20.0000 chunk 532 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 323 optimal weight: 6.9990 chunk 396 optimal weight: 0.9990 chunk 616 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN B 103 ASN ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS F 32 ASN F 139 GLN H 89 GLN ** N 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 GLN Q 209 ASN ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 199 GLN R 209 ASN S 36 HIS S 69 HIS S 98 ASN S 130 GLN S 188 ASN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 5 GLN U 71 HIS W 38 ASN W 139 GLN X 104 HIS ** Y 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 80 HIS b 15 ASN b 44 HIS b 80 ASN c 48 HIS c 99 ASN d 22 GLN d 29 HIS d 63 GLN t 53 GLN ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 127 HIS t 194 ASN t 199 HIS t 290 ASN t 509 ASN t 547 ASN t 595 ASN t 664 GLN t 706 HIS g 5 HIS ** p 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 46 GLN r 222 ASN r 270 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 80787 Z= 0.206 Angle : 0.774 15.006 117118 Z= 0.399 Chirality : 0.043 0.331 14414 Planarity : 0.006 0.094 8812 Dihedral : 24.570 179.905 31577 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.78 % Favored : 89.75 % Rotamer: Outliers : 3.65 % Allowed : 12.59 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 2.25 % Twisted General : 0.58 % 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: -3.40 (0.10), residues: 5153 helix: -1.69 (0.11), residues: 1657 sheet: -1.97 (0.18), residues: 735 loop : -2.76 (0.11), residues: 2761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 46 HIS 0.012 0.001 HIS r 185 PHE 0.028 0.002 PHE U 131 TYR 0.040 0.002 TYR r 10 ARG 0.013 0.001 ARG t 776 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1061 time to evaluate : 4.470 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 GLU cc_start: 0.4238 (OUTLIER) cc_final: 0.3924 (pp20) REVERT: B 46 TRP cc_start: 0.6746 (m-90) cc_final: 0.6203 (m-10) REVERT: B 54 LYS cc_start: 0.4450 (mtpp) cc_final: 0.3964 (ptpp) REVERT: B 81 ARG cc_start: 0.6688 (mtp85) cc_final: 0.6429 (ttt-90) REVERT: B 126 ASP cc_start: 0.6605 (m-30) cc_final: 0.6372 (m-30) REVERT: C 46 LEU cc_start: 0.4577 (tt) cc_final: 0.4296 (mp) REVERT: C 85 VAL cc_start: 0.6521 (t) cc_final: 0.6118 (t) REVERT: E 22 LEU cc_start: 0.7885 (mt) cc_final: 0.7411 (tt) REVERT: E 49 MET cc_start: 0.4569 (OUTLIER) cc_final: 0.3886 (pmm) REVERT: E 77 ARG cc_start: 0.8213 (ptp90) cc_final: 0.7991 (pmt-80) REVERT: E 87 PRO cc_start: 0.7294 (Cg_exo) cc_final: 0.6904 (Cg_endo) REVERT: F 116 LEU cc_start: 0.6177 (mp) cc_final: 0.5328 (tp) REVERT: H 56 LYS cc_start: 0.6323 (ttmt) cc_final: 0.5669 (mmtp) REVERT: H 73 MET cc_start: 0.7976 (mtt) cc_final: 0.7619 (mmm) REVERT: I 67 MET cc_start: 0.7917 (mtt) cc_final: 0.7681 (mpp) REVERT: I 92 LYS cc_start: 0.6595 (tptp) cc_final: 0.6337 (tppp) REVERT: I 133 ASP cc_start: 0.6766 (m-30) cc_final: 0.6442 (t0) REVERT: I 134 ARG cc_start: 0.7359 (ptm-80) cc_final: 0.6761 (mmm160) REVERT: L 27 GLN cc_start: 0.7626 (mt0) cc_final: 0.7214 (mm-40) REVERT: L 57 MET cc_start: 0.5346 (ttm) cc_final: 0.5131 (tmm) REVERT: N 143 LYS cc_start: -0.0987 (OUTLIER) cc_final: -0.1300 (tmtm) REVERT: P 7 PHE cc_start: 0.8157 (m-80) cc_final: 0.7920 (m-80) REVERT: P 8 ASP cc_start: 0.8882 (m-30) cc_final: 0.8455 (t0) REVERT: P 27 ARG cc_start: 0.7417 (tpp80) cc_final: 0.7021 (tmt170) REVERT: P 38 PHE cc_start: 0.8971 (t80) cc_final: 0.8670 (t80) REVERT: P 43 ASP cc_start: 0.7699 (m-30) cc_final: 0.7288 (t0) REVERT: P 117 GLU cc_start: 0.8998 (tt0) cc_final: 0.8378 (pm20) REVERT: P 123 VAL cc_start: 0.8953 (t) cc_final: 0.8547 (m) REVERT: P 125 ASP cc_start: 0.8698 (t0) cc_final: 0.8359 (t0) REVERT: P 128 SER cc_start: 0.8570 (m) cc_final: 0.8195 (p) REVERT: P 198 MET cc_start: 0.9211 (mmm) cc_final: 0.8990 (ttm) REVERT: Q 26 ARG cc_start: 0.8480 (ptp-170) cc_final: 0.8242 (mpp-170) REVERT: Q 30 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: Q 82 ARG cc_start: 0.8414 (mtp85) cc_final: 0.7868 (mtm180) REVERT: Q 103 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8052 (tmm) REVERT: Q 104 ASP cc_start: 0.8868 (t0) cc_final: 0.8627 (t0) REVERT: Q 131 ASP cc_start: 0.6916 (p0) cc_final: 0.6630 (p0) REVERT: Q 152 ARG cc_start: 0.8689 (ttt180) cc_final: 0.8362 (ttp-110) REVERT: Q 198 GLU cc_start: 0.8820 (tp30) cc_final: 0.8387 (mp0) REVERT: R 88 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.6422 (pttt) REVERT: R 120 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8741 (pt0) REVERT: R 137 ILE cc_start: 0.8929 (tt) cc_final: 0.8644 (pt) REVERT: R 176 SER cc_start: 0.9241 (m) cc_final: 0.8471 (t) REVERT: R 206 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8118 (m) REVERT: S 118 GLU cc_start: 0.8936 (tt0) cc_final: 0.8650 (mp0) REVERT: S 225 VAL cc_start: 0.9092 (t) cc_final: 0.8885 (p) REVERT: T 2 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7641 (mptt) REVERT: T 23 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7578 (ttm170) REVERT: T 29 ASP cc_start: 0.8869 (m-30) cc_final: 0.8462 (t0) REVERT: T 37 ASP cc_start: 0.8204 (m-30) cc_final: 0.7964 (m-30) REVERT: T 97 VAL cc_start: 0.8493 (t) cc_final: 0.8228 (m) REVERT: T 118 GLU cc_start: 0.7236 (pt0) cc_final: 0.6466 (mm-30) REVERT: T 150 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8335 (pp20) REVERT: T 151 ASP cc_start: 0.7540 (m-30) cc_final: 0.6650 (m-30) REVERT: T 190 GLN cc_start: 0.8597 (mm110) cc_final: 0.8334 (tm-30) REVERT: U 9 LEU cc_start: 0.6354 (mt) cc_final: 0.5923 (tt) REVERT: U 16 LEU cc_start: 0.7714 (mt) cc_final: 0.7466 (tp) REVERT: U 46 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6696 (mt) REVERT: U 70 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7556 (t80) REVERT: U 72 LYS cc_start: 0.8038 (mttt) cc_final: 0.7777 (mmmt) REVERT: U 89 HIS cc_start: 0.8609 (m170) cc_final: 0.8133 (m-70) REVERT: U 95 GLU cc_start: 0.7327 (tp30) cc_final: 0.6652 (pp20) REVERT: U 158 ASP cc_start: 0.8182 (m-30) cc_final: 0.7893 (m-30) REVERT: U 167 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8697 (mm-30) REVERT: U 184 GLU cc_start: 0.8104 (tt0) cc_final: 0.7866 (tm-30) REVERT: V 46 VAL cc_start: 0.8578 (p) cc_final: 0.8362 (m) REVERT: V 64 ASN cc_start: 0.8592 (t0) cc_final: 0.8304 (t0) REVERT: V 77 ARG cc_start: 0.8503 (ttp-170) cc_final: 0.8292 (ptm160) REVERT: V 179 CYS cc_start: 0.9194 (t) cc_final: 0.8853 (t) REVERT: W 28 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8003 (tt) REVERT: W 33 GLU cc_start: 0.8287 (tt0) cc_final: 0.7950 (tp30) REVERT: W 54 ARG cc_start: 0.8739 (ttp80) cc_final: 0.8343 (ttm170) REVERT: W 64 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7797 (mm-30) REVERT: W 72 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8597 (tm-30) REVERT: W 157 ASP cc_start: 0.7895 (t0) cc_final: 0.7266 (p0) REVERT: X 116 ARG cc_start: 0.8921 (mtt90) cc_final: 0.8607 (tpt-90) REVERT: X 118 GLN cc_start: 0.7959 (tt0) cc_final: 0.7629 (pt0) REVERT: Y 33 VAL cc_start: 0.8426 (m) cc_final: 0.7967 (p) REVERT: Y 49 GLN cc_start: 0.8519 (mt0) cc_final: 0.8256 (mt0) REVERT: Y 64 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7532 (mtm-85) REVERT: Y 80 LEU cc_start: 0.8277 (mp) cc_final: 0.8075 (tp) REVERT: Y 112 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8266 (tttt) REVERT: Y 141 TYR cc_start: 0.8887 (t80) cc_final: 0.8187 (t80) REVERT: Z 96 PRO cc_start: 0.8070 (Cg_exo) cc_final: 0.7832 (Cg_endo) REVERT: Z 116 GLU cc_start: 0.7948 (pt0) cc_final: 0.7671 (pt0) REVERT: a 2 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8514 (mp0) REVERT: a 85 TYR cc_start: 0.8300 (t80) cc_final: 0.7985 (t80) REVERT: b 16 ASN cc_start: 0.9338 (m-40) cc_final: 0.8976 (m-40) REVERT: b 24 GLN cc_start: 0.8884 (pm20) cc_final: 0.8566 (pm20) REVERT: b 104 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8465 (pp) REVERT: c 30 LYS cc_start: 0.8562 (tppp) cc_final: 0.8328 (tptt) REVERT: c 55 GLU cc_start: 0.7623 (pt0) cc_final: 0.7223 (tp30) REVERT: c 94 ASN cc_start: 0.7832 (m-40) cc_final: 0.7549 (p0) REVERT: c 99 ASN cc_start: 0.7703 (m110) cc_final: 0.7417 (t0) REVERT: d 32 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7905 (ttp80) REVERT: d 42 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8677 (tp30) REVERT: d 63 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8385 (tt0) REVERT: d 106 GLN cc_start: 0.8520 (pt0) cc_final: 0.8065 (mt0) REVERT: f 79 PHE cc_start: 0.8246 (p90) cc_final: 0.7650 (p90) REVERT: t 121 LYS cc_start: 0.6480 (mmtt) cc_final: 0.6110 (mttt) REVERT: t 132 LYS cc_start: 0.7690 (tttp) cc_final: 0.7461 (tptp) REVERT: t 188 TYR cc_start: 0.8927 (p90) cc_final: 0.8597 (p90) REVERT: t 218 HIS cc_start: 0.7656 (m-70) cc_final: 0.7355 (t-90) REVERT: t 220 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7502 (p90) REVERT: t 248 ARG cc_start: 0.6398 (ptp-170) cc_final: 0.5755 (ptp90) REVERT: t 342 ASN cc_start: 0.8024 (m-40) cc_final: 0.7749 (t0) REVERT: t 525 TRP cc_start: 0.8325 (t-100) cc_final: 0.7932 (t-100) REVERT: t 558 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7597 (mtm180) REVERT: t 582 TYR cc_start: 0.8706 (m-80) cc_final: 0.8446 (m-80) REVERT: t 638 ASN cc_start: 0.8632 (t0) cc_final: 0.8155 (t0) REVERT: t 720 MET cc_start: 0.6837 (mmm) cc_final: 0.6396 (mmm) REVERT: t 721 PHE cc_start: 0.8254 (m-10) cc_final: 0.7855 (m-80) REVERT: t 754 TYR cc_start: 0.7857 (m-10) cc_final: 0.7111 (m-80) REVERT: t 769 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7475 (p) REVERT: t 780 MET cc_start: 0.7680 (mmt) cc_final: 0.7380 (tpt) REVERT: g 26 LYS cc_start: 0.6623 (ptmt) cc_final: 0.6353 (mmtm) REVERT: p 125 LYS cc_start: 0.8405 (mptt) cc_final: 0.8116 (ptpp) REVERT: p 196 ASP cc_start: 0.8402 (m-30) cc_final: 0.8033 (t70) REVERT: p 221 ARG cc_start: 0.6656 (mtm-85) cc_final: 0.6267 (mtp-110) REVERT: p 264 ARG cc_start: 0.6204 (mmt90) cc_final: 0.5977 (ptt180) REVERT: p 269 ARG cc_start: 0.5736 (ptt180) cc_final: 0.5249 (ttp-170) REVERT: r 1 MET cc_start: 0.2034 (mmm) cc_final: 0.1171 (ttp) REVERT: r 65 MET cc_start: 0.2769 (mmp) cc_final: 0.1573 (ttp) REVERT: r 184 ARG cc_start: 0.4415 (OUTLIER) cc_final: 0.4211 (mtt-85) outliers start: 152 outliers final: 64 residues processed: 1153 average time/residue: 0.8567 time to fit residues: 1667.1584 Evaluate side-chains 928 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 849 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain Q residue 30 PHE Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain Q residue 216 LYS Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 206 ASP Chi-restraints excluded: chain S residue 253 ASP Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 70 PHE Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 70 ILE Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain b residue 83 ILE Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 40 CYS Chi-restraints excluded: chain t residue 70 ILE Chi-restraints excluded: chain t residue 99 ASP Chi-restraints excluded: chain t residue 150 ASP Chi-restraints excluded: chain t residue 220 PHE Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 482 PHE Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 545 THR Chi-restraints excluded: chain t residue 612 GLU Chi-restraints excluded: chain t residue 656 CYS Chi-restraints excluded: chain t residue 665 SER Chi-restraints excluded: chain t residue 681 GLU Chi-restraints excluded: chain t residue 722 PHE Chi-restraints excluded: chain t residue 769 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain p residue 98 LYS Chi-restraints excluded: chain p residue 164 LEU Chi-restraints excluded: chain p residue 192 THR Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain p residue 262 ASN Chi-restraints excluded: chain r residue 92 ASP Chi-restraints excluded: chain r residue 124 ILE Chi-restraints excluded: chain r residue 155 SER Chi-restraints excluded: chain r residue 184 ARG Chi-restraints excluded: chain r residue 206 ILE Chi-restraints excluded: chain r residue 217 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 342 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 513 optimal weight: 7.9990 chunk 419 optimal weight: 0.8980 chunk 170 optimal weight: 20.0000 chunk 617 optimal weight: 0.9990 chunk 667 optimal weight: 30.0000 chunk 550 optimal weight: 4.9990 chunk 612 optimal weight: 5.9990 chunk 210 optimal weight: 40.0000 chunk 495 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN I 25 GLN ** N 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN P 131 GLN ** Q 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN Y 5 HIS Y 101 HIS ** a 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 194 ASN t 290 ASN ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 595 ASN t 599 GLN t 631 GLN t 706 HIS ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 80787 Z= 0.319 Angle : 0.787 15.625 117118 Z= 0.403 Chirality : 0.044 0.329 14414 Planarity : 0.006 0.064 8812 Dihedral : 24.370 178.150 31559 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.53 % Favored : 88.07 % Rotamer: Outliers : 5.23 % Allowed : 15.25 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 1.35 % Twisted General : 0.52 % 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: -2.90 (0.11), residues: 5153 helix: -0.95 (0.12), residues: 1661 sheet: -1.90 (0.18), residues: 723 loop : -2.62 (0.11), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 46 HIS 0.014 0.002 HIS r 185 PHE 0.036 0.002 PHE r 233 TYR 0.031 0.002 TYR r 10 ARG 0.011 0.001 ARG t 502 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 877 time to evaluate : 4.490 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 GLU cc_start: 0.4117 (OUTLIER) cc_final: 0.3830 (pp20) REVERT: B 46 TRP cc_start: 0.6777 (m-90) cc_final: 0.6116 (m-10) REVERT: B 54 LYS cc_start: 0.4074 (mtpp) cc_final: 0.3532 (ptpp) REVERT: B 72 HIS cc_start: 0.7435 (t-90) cc_final: 0.7000 (t-170) REVERT: B 109 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7997 (ttmm) REVERT: E 22 LEU cc_start: 0.7867 (mt) cc_final: 0.7396 (tt) REVERT: E 49 MET cc_start: 0.4384 (OUTLIER) cc_final: 0.4036 (pmm) REVERT: E 81 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7629 (mtp85) REVERT: H 56 LYS cc_start: 0.6215 (ttmt) cc_final: 0.5592 (mmtp) REVERT: H 73 MET cc_start: 0.7836 (mtt) cc_final: 0.7581 (mmt) REVERT: I 134 ARG cc_start: 0.7521 (ptm-80) cc_final: 0.6888 (mmm160) REVERT: L 27 GLN cc_start: 0.7580 (mt0) cc_final: 0.7192 (mm-40) REVERT: P 7 PHE cc_start: 0.8308 (m-80) cc_final: 0.8036 (m-80) REVERT: P 27 ARG cc_start: 0.7470 (tpp80) cc_final: 0.7077 (tmt170) REVERT: P 38 PHE cc_start: 0.9028 (t80) cc_final: 0.8779 (t80) REVERT: P 43 ASP cc_start: 0.7931 (m-30) cc_final: 0.7526 (t0) REVERT: P 117 GLU cc_start: 0.9036 (tt0) cc_final: 0.8541 (pm20) REVERT: P 123 VAL cc_start: 0.9132 (t) cc_final: 0.8685 (m) REVERT: P 125 ASP cc_start: 0.8629 (t0) cc_final: 0.8400 (t0) REVERT: P 128 SER cc_start: 0.8659 (m) cc_final: 0.8272 (p) REVERT: P 135 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7837 (tp30) REVERT: P 198 MET cc_start: 0.9234 (mmm) cc_final: 0.8994 (ttm) REVERT: Q 26 ARG cc_start: 0.8488 (ptp-170) cc_final: 0.8235 (ptt-90) REVERT: Q 30 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: Q 82 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8260 (mtp85) REVERT: Q 131 ASP cc_start: 0.7042 (p0) cc_final: 0.6759 (p0) REVERT: Q 152 ARG cc_start: 0.8638 (ttt180) cc_final: 0.8289 (ttp-110) REVERT: Q 158 SER cc_start: 0.9213 (m) cc_final: 0.8986 (p) REVERT: Q 181 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8553 (mt) REVERT: Q 198 GLU cc_start: 0.8734 (tp30) cc_final: 0.8337 (mp0) REVERT: R 76 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8613 (mp) REVERT: R 88 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6383 (pttt) REVERT: R 120 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8687 (pt0) REVERT: R 176 SER cc_start: 0.9225 (m) cc_final: 0.8585 (t) REVERT: S 118 GLU cc_start: 0.9038 (tt0) cc_final: 0.8719 (tm-30) REVERT: T 2 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7695 (mptt) REVERT: T 37 ASP cc_start: 0.8257 (m-30) cc_final: 0.8052 (m-30) REVERT: T 97 VAL cc_start: 0.8578 (t) cc_final: 0.8320 (m) REVERT: T 118 GLU cc_start: 0.7279 (pt0) cc_final: 0.6553 (mm-30) REVERT: T 150 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8312 (pp20) REVERT: T 151 ASP cc_start: 0.7770 (m-30) cc_final: 0.6918 (m-30) REVERT: T 190 GLN cc_start: 0.8591 (mm110) cc_final: 0.8276 (tm-30) REVERT: T 203 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8329 (tm-30) REVERT: U 16 LEU cc_start: 0.7744 (mt) cc_final: 0.7435 (tt) REVERT: U 46 ILE cc_start: 0.6654 (OUTLIER) cc_final: 0.6369 (mt) REVERT: U 70 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7648 (t80) REVERT: U 72 LYS cc_start: 0.7930 (mttt) cc_final: 0.7686 (mmmt) REVERT: U 95 GLU cc_start: 0.7491 (tp30) cc_final: 0.6734 (pp20) REVERT: U 158 ASP cc_start: 0.8392 (m-30) cc_final: 0.8121 (m-30) REVERT: U 167 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8655 (mm-30) REVERT: U 184 GLU cc_start: 0.8113 (tt0) cc_final: 0.7808 (tm-30) REVERT: V 46 VAL cc_start: 0.8501 (p) cc_final: 0.8236 (m) REVERT: V 64 ASN cc_start: 0.8680 (t0) cc_final: 0.8284 (t0) REVERT: V 77 ARG cc_start: 0.8472 (ttp-170) cc_final: 0.8218 (mtp-110) REVERT: V 153 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6611 (mt-10) REVERT: V 179 CYS cc_start: 0.9216 (t) cc_final: 0.8868 (t) REVERT: W 33 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7961 (tp30) REVERT: W 54 ARG cc_start: 0.8809 (ttp80) cc_final: 0.8491 (ttm-80) REVERT: W 64 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7951 (mm-30) REVERT: W 72 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8776 (tm-30) REVERT: W 88 GLU cc_start: 0.9269 (mp0) cc_final: 0.8608 (pp20) REVERT: X 22 ASN cc_start: 0.8631 (t0) cc_final: 0.8309 (t0) REVERT: X 116 ARG cc_start: 0.8896 (mtt90) cc_final: 0.8557 (tpt-90) REVERT: X 118 GLN cc_start: 0.7963 (tt0) cc_final: 0.7717 (pt0) REVERT: Y 9 LYS cc_start: 0.9221 (mmtt) cc_final: 0.8440 (tptt) REVERT: Y 33 VAL cc_start: 0.8602 (m) cc_final: 0.8125 (p) REVERT: Y 49 GLN cc_start: 0.8617 (mt0) cc_final: 0.8367 (mt0) REVERT: Y 141 TYR cc_start: 0.8830 (t80) cc_final: 0.8392 (t80) REVERT: Z 99 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7949 (mp10) REVERT: a 2 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8501 (mp0) REVERT: b 12 ASN cc_start: 0.9112 (t0) cc_final: 0.8907 (t0) REVERT: b 16 ASN cc_start: 0.9321 (m-40) cc_final: 0.8983 (m-40) REVERT: b 24 GLN cc_start: 0.8897 (pm20) cc_final: 0.8517 (pm20) REVERT: b 104 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8636 (pp) REVERT: b 115 GLU cc_start: 0.9243 (tt0) cc_final: 0.8787 (tm-30) REVERT: c 30 LYS cc_start: 0.8595 (tppp) cc_final: 0.8263 (mmtt) REVERT: c 55 GLU cc_start: 0.7911 (pt0) cc_final: 0.7479 (tp30) REVERT: c 94 ASN cc_start: 0.7937 (m-40) cc_final: 0.7698 (p0) REVERT: c 99 ASN cc_start: 0.8007 (m110) cc_final: 0.7531 (t0) REVERT: d 32 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8021 (ttp80) REVERT: d 42 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8540 (tm-30) REVERT: d 63 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8441 (tt0) REVERT: d 106 GLN cc_start: 0.8799 (pt0) cc_final: 0.8398 (mt0) REVERT: f 6 ASP cc_start: 0.8352 (m-30) cc_final: 0.7932 (m-30) REVERT: f 75 GLU cc_start: 0.8482 (pp20) cc_final: 0.8270 (pp20) REVERT: f 79 PHE cc_start: 0.8153 (p90) cc_final: 0.7760 (p90) REVERT: t 121 LYS cc_start: 0.6440 (mmtt) cc_final: 0.6155 (mttt) REVERT: t 188 TYR cc_start: 0.9105 (p90) cc_final: 0.8847 (p90) REVERT: t 218 HIS cc_start: 0.7681 (m-70) cc_final: 0.7380 (t-90) REVERT: t 220 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7992 (p90) REVERT: t 248 ARG cc_start: 0.6552 (ptp-170) cc_final: 0.5728 (ptp90) REVERT: t 342 ASN cc_start: 0.8048 (m-40) cc_final: 0.7660 (t0) REVERT: t 525 TRP cc_start: 0.8461 (t-100) cc_final: 0.8114 (t-100) REVERT: t 558 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7693 (mtm180) REVERT: t 643 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7739 (mt-10) REVERT: t 649 ASP cc_start: 0.6814 (p0) cc_final: 0.6565 (p0) REVERT: t 695 ARG cc_start: 0.8497 (tpt90) cc_final: 0.7929 (tpp80) REVERT: t 721 PHE cc_start: 0.8489 (m-10) cc_final: 0.7902 (m-10) REVERT: t 752 HIS cc_start: 0.6816 (m170) cc_final: 0.5600 (m90) REVERT: t 754 TYR cc_start: 0.7926 (m-10) cc_final: 0.7263 (m-80) REVERT: t 780 MET cc_start: 0.7822 (mmt) cc_final: 0.7415 (tpt) REVERT: g 26 LYS cc_start: 0.6553 (ptmt) cc_final: 0.6273 (mmtm) REVERT: p 124 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7276 (pp) REVERT: p 125 LYS cc_start: 0.8436 (mptt) cc_final: 0.8190 (pttm) REVERT: p 196 ASP cc_start: 0.8637 (m-30) cc_final: 0.8335 (t70) REVERT: p 221 ARG cc_start: 0.6712 (mtm-85) cc_final: 0.6369 (mtp-110) REVERT: p 264 ARG cc_start: 0.6313 (mmt90) cc_final: 0.5999 (ptt180) REVERT: p 269 ARG cc_start: 0.5280 (ptt180) cc_final: 0.4810 (ttp-170) REVERT: r 65 MET cc_start: 0.2623 (mmp) cc_final: 0.1505 (ttp) REVERT: r 184 ARG cc_start: 0.4599 (mtm-85) cc_final: 0.4327 (ttp-110) outliers start: 218 outliers final: 133 residues processed: 1021 average time/residue: 0.7457 time to fit residues: 1286.0874 Evaluate side-chains 932 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 783 time to evaluate : 4.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 135 GLU Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain Q residue 30 PHE Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 82 ASN Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 206 ASP Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain S residue 253 ASP Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 127 THR Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 168 THR Chi-restraints excluded: chain T residue 180 THR Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 70 PHE Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 166 LEU Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain V residue 153 GLU Chi-restraints excluded: chain V residue 188 GLU Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Z residue 99 GLN Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 83 ILE Chi-restraints excluded: chain b residue 94 LEU Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 128 SER Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 40 CYS Chi-restraints excluded: chain f residue 55 THR Chi-restraints excluded: chain t residue 70 ILE Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 99 ASP Chi-restraints excluded: chain t residue 133 SER Chi-restraints excluded: chain t residue 148 ILE Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 206 LEU Chi-restraints excluded: chain t residue 208 VAL Chi-restraints excluded: chain t residue 220 PHE Chi-restraints excluded: chain t residue 262 ASP Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 482 PHE Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 545 THR Chi-restraints excluded: chain t residue 612 GLU Chi-restraints excluded: chain t residue 620 VAL Chi-restraints excluded: chain t residue 657 ILE Chi-restraints excluded: chain t residue 665 SER Chi-restraints excluded: chain t residue 681 GLU Chi-restraints excluded: chain t residue 706 HIS Chi-restraints excluded: chain t residue 735 LEU Chi-restraints excluded: chain t residue 737 THR Chi-restraints excluded: chain t residue 751 THR Chi-restraints excluded: chain t residue 771 MET Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain p residue 98 LYS Chi-restraints excluded: chain p residue 124 LEU Chi-restraints excluded: chain p residue 164 LEU Chi-restraints excluded: chain p residue 192 THR Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain p residue 239 HIS Chi-restraints excluded: chain p residue 262 ASN Chi-restraints excluded: chain r residue 32 VAL Chi-restraints excluded: chain r residue 92 ASP Chi-restraints excluded: chain r residue 113 SER Chi-restraints excluded: chain r residue 124 ILE Chi-restraints excluded: chain r residue 155 SER Chi-restraints excluded: chain r residue 157 LEU Chi-restraints excluded: chain r residue 182 ASN Chi-restraints excluded: chain r residue 250 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 610 optimal weight: 0.8980 chunk 464 optimal weight: 5.9990 chunk 320 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 294 optimal weight: 3.9990 chunk 414 optimal weight: 9.9990 chunk 619 optimal weight: 3.9990 chunk 656 optimal weight: 40.0000 chunk 323 optimal weight: 3.9990 chunk 587 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 HIS ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN Q 211 HIS ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN ** V 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 HIS ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 290 ASN ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 599 GLN ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 153 HIS ** r 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 80787 Z= 0.254 Angle : 0.727 15.679 117118 Z= 0.374 Chirality : 0.042 0.317 14414 Planarity : 0.005 0.066 8812 Dihedral : 24.228 179.862 31553 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.20 % Favored : 88.43 % Rotamer: Outliers : 5.11 % Allowed : 17.60 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 1.35 % Twisted General : 0.44 % 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: -2.60 (0.11), residues: 5153 helix: -0.52 (0.13), residues: 1675 sheet: -1.84 (0.19), residues: 696 loop : -2.54 (0.11), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP t 778 HIS 0.014 0.001 HIS r 185 PHE 0.026 0.002 PHE r 279 TYR 0.031 0.002 TYR R 243 ARG 0.007 0.001 ARG t 502 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 865 time to evaluate : 4.486 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: symmetry clash REVERT: D 25 GLU cc_start: 0.4196 (OUTLIER) cc_final: 0.3918 (pp20) REVERT: B 46 TRP cc_start: 0.6613 (m-90) cc_final: 0.6147 (m-10) REVERT: B 54 LYS cc_start: 0.4175 (mtpp) cc_final: 0.3618 (ptpp) REVERT: B 72 HIS cc_start: 0.7540 (t-90) cc_final: 0.7209 (t70) REVERT: E 22 LEU cc_start: 0.7823 (mt) cc_final: 0.7324 (tt) REVERT: H 56 LYS cc_start: 0.6207 (ttmt) cc_final: 0.5616 (mmtp) REVERT: H 73 MET cc_start: 0.7810 (mtt) cc_final: 0.7594 (mmt) REVERT: H 109 LEU cc_start: 0.5947 (tp) cc_final: 0.5734 (pp) REVERT: I 67 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7309 (mpp) REVERT: I 95 ASP cc_start: 0.6223 (m-30) cc_final: 0.5764 (p0) REVERT: I 134 ARG cc_start: 0.7522 (ptm-80) cc_final: 0.6795 (mmm160) REVERT: L 27 GLN cc_start: 0.7625 (mt0) cc_final: 0.7206 (mm-40) REVERT: P 27 ARG cc_start: 0.7422 (tpp80) cc_final: 0.7001 (tmt170) REVERT: P 38 PHE cc_start: 0.9022 (t80) cc_final: 0.8795 (t80) REVERT: P 43 ASP cc_start: 0.7826 (m-30) cc_final: 0.7443 (t0) REVERT: P 117 GLU cc_start: 0.9017 (tt0) cc_final: 0.8537 (pm20) REVERT: P 123 VAL cc_start: 0.9111 (t) cc_final: 0.8688 (m) REVERT: P 128 SER cc_start: 0.8675 (m) cc_final: 0.8308 (p) REVERT: P 135 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: P 148 ASP cc_start: 0.8773 (p0) cc_final: 0.8552 (p0) REVERT: P 160 ILE cc_start: 0.8891 (mm) cc_final: 0.8678 (mm) REVERT: Q 26 ARG cc_start: 0.8487 (ptp-170) cc_final: 0.8255 (ptt-90) REVERT: Q 30 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: Q 82 ARG cc_start: 0.8579 (mtp85) cc_final: 0.8213 (mtp85) REVERT: Q 131 ASP cc_start: 0.6606 (p0) cc_final: 0.6314 (p0) REVERT: Q 152 ARG cc_start: 0.8690 (ttt180) cc_final: 0.8338 (ttp-110) REVERT: Q 181 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8447 (mt) REVERT: Q 198 GLU cc_start: 0.8693 (tp30) cc_final: 0.8280 (mt-10) REVERT: R 76 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8639 (mp) REVERT: R 88 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6391 (pttt) REVERT: R 120 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8681 (pt0) REVERT: R 176 SER cc_start: 0.9209 (m) cc_final: 0.8600 (t) REVERT: S 118 GLU cc_start: 0.8998 (tt0) cc_final: 0.8706 (tm-30) REVERT: S 136 VAL cc_start: 0.9198 (t) cc_final: 0.8986 (p) REVERT: T 2 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7671 (mptt) REVERT: T 37 ASP cc_start: 0.8401 (m-30) cc_final: 0.8163 (m-30) REVERT: T 61 PHE cc_start: 0.8948 (m-80) cc_final: 0.8637 (m-10) REVERT: T 85 ARG cc_start: 0.9167 (ttp80) cc_final: 0.8862 (ttp80) REVERT: T 97 VAL cc_start: 0.8537 (t) cc_final: 0.8278 (m) REVERT: T 118 GLU cc_start: 0.7380 (pt0) cc_final: 0.6506 (mm-30) REVERT: T 150 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8268 (pp20) REVERT: T 151 ASP cc_start: 0.7752 (m-30) cc_final: 0.6865 (m-30) REVERT: T 152 ASP cc_start: 0.7696 (t0) cc_final: 0.7230 (t0) REVERT: T 201 GLN cc_start: 0.8924 (mm110) cc_final: 0.8388 (mp10) REVERT: T 203 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8413 (tm-30) REVERT: U 16 LEU cc_start: 0.7757 (mt) cc_final: 0.7446 (tt) REVERT: U 46 ILE cc_start: 0.6721 (OUTLIER) cc_final: 0.6217 (mt) REVERT: U 70 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7578 (t80) REVERT: U 72 LYS cc_start: 0.7953 (mttt) cc_final: 0.7679 (mmmt) REVERT: U 95 GLU cc_start: 0.7432 (tp30) cc_final: 0.6641 (pp20) REVERT: U 158 ASP cc_start: 0.8413 (m-30) cc_final: 0.8133 (m-30) REVERT: U 167 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8616 (mm-30) REVERT: U 184 GLU cc_start: 0.8098 (tt0) cc_final: 0.7806 (tm-30) REVERT: V 46 VAL cc_start: 0.8322 (p) cc_final: 0.8039 (m) REVERT: V 64 ASN cc_start: 0.8672 (t0) cc_final: 0.8282 (t0) REVERT: V 77 ARG cc_start: 0.8409 (ttp-170) cc_final: 0.8176 (mtp-110) REVERT: V 153 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6871 (mt-10) REVERT: V 179 CYS cc_start: 0.9279 (t) cc_final: 0.8894 (t) REVERT: W 33 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7869 (tp30) REVERT: W 54 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8394 (ttm170) REVERT: W 64 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7944 (mm-30) REVERT: W 88 GLU cc_start: 0.9286 (mp0) cc_final: 0.8613 (pp20) REVERT: X 22 ASN cc_start: 0.8566 (t0) cc_final: 0.8266 (t0) REVERT: X 116 ARG cc_start: 0.8902 (mtt90) cc_final: 0.8594 (tpt-90) REVERT: Y 9 LYS cc_start: 0.9180 (mmtt) cc_final: 0.8411 (tptt) REVERT: Y 33 VAL cc_start: 0.8661 (m) cc_final: 0.8346 (p) REVERT: Y 49 GLN cc_start: 0.8594 (mt0) cc_final: 0.8352 (mt0) REVERT: Y 141 TYR cc_start: 0.8770 (t80) cc_final: 0.8343 (t80) REVERT: Z 20 TYR cc_start: 0.7186 (t80) cc_final: 0.6805 (t80) REVERT: a 2 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8566 (mm-30) REVERT: a 7 GLN cc_start: 0.8265 (mt0) cc_final: 0.7979 (mp10) REVERT: a 49 GLU cc_start: 0.8794 (tp30) cc_final: 0.8432 (tp30) REVERT: b 16 ASN cc_start: 0.9349 (m-40) cc_final: 0.9038 (m-40) REVERT: b 24 GLN cc_start: 0.8937 (pm20) cc_final: 0.8572 (pm20) REVERT: b 104 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8575 (pp) REVERT: b 115 GLU cc_start: 0.9180 (tt0) cc_final: 0.8790 (tm-30) REVERT: c 30 LYS cc_start: 0.8585 (tppp) cc_final: 0.8280 (mmtt) REVERT: c 55 GLU cc_start: 0.7969 (pt0) cc_final: 0.7535 (tp30) REVERT: c 94 ASN cc_start: 0.7946 (m-40) cc_final: 0.7685 (p0) REVERT: c 99 ASN cc_start: 0.8026 (m110) cc_final: 0.7528 (t0) REVERT: d 3 ASP cc_start: 0.4507 (t70) cc_final: 0.4182 (t70) REVERT: d 42 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8538 (tm-30) REVERT: d 63 GLN cc_start: 0.8882 (tp-100) cc_final: 0.8461 (tt0) REVERT: d 106 GLN cc_start: 0.8814 (pt0) cc_final: 0.8441 (mm-40) REVERT: f 6 ASP cc_start: 0.8211 (m-30) cc_final: 0.7963 (m-30) REVERT: f 79 PHE cc_start: 0.8144 (p90) cc_final: 0.7773 (p90) REVERT: t 121 LYS cc_start: 0.6411 (mmtt) cc_final: 0.6117 (mttt) REVERT: t 218 HIS cc_start: 0.7815 (m-70) cc_final: 0.7436 (t-90) REVERT: t 265 ASP cc_start: 0.8313 (t0) cc_final: 0.8053 (t70) REVERT: t 525 TRP cc_start: 0.8420 (t-100) cc_final: 0.8064 (t-100) REVERT: t 588 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8525 (mm-30) REVERT: t 643 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7638 (mm-30) REVERT: t 695 ARG cc_start: 0.8601 (tpt90) cc_final: 0.8007 (tpp80) REVERT: t 752 HIS cc_start: 0.6749 (m170) cc_final: 0.5552 (m90) REVERT: t 754 TYR cc_start: 0.7929 (m-10) cc_final: 0.7348 (m-80) REVERT: t 780 MET cc_start: 0.7865 (mmt) cc_final: 0.7445 (tpt) REVERT: g 26 LYS cc_start: 0.6685 (ptmt) cc_final: 0.6399 (mmtm) REVERT: p 124 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7204 (pp) REVERT: p 125 LYS cc_start: 0.8401 (mptt) cc_final: 0.8197 (pttm) REVERT: p 196 ASP cc_start: 0.8640 (m-30) cc_final: 0.8363 (t70) REVERT: p 221 ARG cc_start: 0.6770 (mtm-85) cc_final: 0.6450 (mtp-110) REVERT: p 264 ARG cc_start: 0.6343 (mmt90) cc_final: 0.6026 (ptt180) REVERT: p 269 ARG cc_start: 0.4932 (ptt180) cc_final: 0.4484 (ttp-170) REVERT: r 65 MET cc_start: 0.2338 (OUTLIER) cc_final: 0.1320 (ttp) REVERT: r 184 ARG cc_start: 0.4721 (mtm-85) cc_final: 0.4467 (ttp-110) outliers start: 213 outliers final: 136 residues processed: 997 average time/residue: 0.7421 time to fit residues: 1261.5714 Evaluate side-chains 939 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 789 time to evaluate : 5.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 67 MET Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 135 GLU Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain Q residue 30 PHE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain S residue 206 ASP Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain S residue 253 ASP Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 127 THR Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 168 THR Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 70 PHE Chi-restraints excluded: chain U residue 77 LEU Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 166 LEU Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain V residue 153 GLU Chi-restraints excluded: chain V residue 188 GLU Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 105 LEU Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 18 HIS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 49 ILE Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain Z residue 99 GLN Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 42 GLN Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 128 SER Chi-restraints excluded: chain d residue 14 SER Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 9 HIS Chi-restraints excluded: chain f residue 26 GLN Chi-restraints excluded: chain f residue 40 CYS Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain t residue 70 ILE Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 99 ASP Chi-restraints excluded: chain t residue 133 SER Chi-restraints excluded: chain t residue 148 ILE Chi-restraints excluded: chain t residue 150 ASP Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 206 LEU Chi-restraints excluded: chain t residue 208 VAL Chi-restraints excluded: chain t residue 220 PHE Chi-restraints excluded: chain t residue 262 ASP Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 482 PHE Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 545 THR Chi-restraints excluded: chain t residue 612 GLU Chi-restraints excluded: chain t residue 620 VAL Chi-restraints excluded: chain t residue 657 ILE Chi-restraints excluded: chain t residue 665 SER Chi-restraints excluded: chain t residue 681 GLU Chi-restraints excluded: chain t residue 735 LEU Chi-restraints excluded: chain t residue 737 THR Chi-restraints excluded: chain t residue 751 THR Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain p residue 98 LYS Chi-restraints excluded: chain p residue 124 LEU Chi-restraints excluded: chain p residue 137 VAL Chi-restraints excluded: chain p residue 164 LEU Chi-restraints excluded: chain p residue 192 THR Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain p residue 239 HIS Chi-restraints excluded: chain p residue 262 ASN Chi-restraints excluded: chain r residue 32 VAL Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain r residue 92 ASP Chi-restraints excluded: chain r residue 124 ILE Chi-restraints excluded: chain r residue 155 SER Chi-restraints excluded: chain r residue 250 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 546 optimal weight: 0.0060 chunk 372 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 488 optimal weight: 0.8980 chunk 270 optimal weight: 6.9990 chunk 560 optimal weight: 6.9990 chunk 453 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 335 optimal weight: 0.9990 chunk 589 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 GLN L 43 ASN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 185 GLN T 189 HIS ** V 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 139 GLN ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 290 ASN ** t 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 640 HIS t 706 HIS ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 203 HIS ** r 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 80787 Z= 0.158 Angle : 0.658 14.242 117118 Z= 0.337 Chirality : 0.039 0.298 14414 Planarity : 0.005 0.061 8812 Dihedral : 23.992 179.592 31553 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.38 % Favored : 89.35 % Rotamer: Outliers : 4.05 % Allowed : 19.54 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 1.35 % Twisted General : 0.34 % 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: -2.22 (0.11), residues: 5153 helix: -0.09 (0.13), residues: 1691 sheet: -1.68 (0.19), residues: 693 loop : -2.39 (0.11), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP t 778 HIS 0.048 0.001 HIS X 18 PHE 0.038 0.002 PHE r 280 TYR 0.028 0.001 TYR R 243 ARG 0.010 0.000 ARG K 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 902 time to evaluate : 4.400 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: symmetry clash revert: symmetry clash REVERT: D 25 GLU cc_start: 0.4371 (OUTLIER) cc_final: 0.4138 (pp20) REVERT: D 54 ARG cc_start: 0.7133 (tpp80) cc_final: 0.6832 (ttm110) REVERT: B 46 TRP cc_start: 0.6329 (m-90) cc_final: 0.5949 (m-10) REVERT: B 54 LYS cc_start: 0.4027 (mtpp) cc_final: 0.3540 (ptpp) REVERT: B 72 HIS cc_start: 0.7617 (t-90) cc_final: 0.7269 (t70) REVERT: B 165 LEU cc_start: 0.7280 (tp) cc_final: 0.6598 (pp) REVERT: B 217 LEU cc_start: 0.7896 (mt) cc_final: 0.7595 (tp) REVERT: E 22 LEU cc_start: 0.7723 (mt) cc_final: 0.7216 (tt) REVERT: E 49 MET cc_start: 0.3657 (mtp) cc_final: 0.3393 (mmp) REVERT: H 56 LYS cc_start: 0.6197 (ttmt) cc_final: 0.5604 (mmtp) REVERT: H 73 MET cc_start: 0.7866 (mtt) cc_final: 0.7628 (mmt) REVERT: I 95 ASP cc_start: 0.5937 (m-30) cc_final: 0.5601 (p0) REVERT: I 134 ARG cc_start: 0.7621 (ptm-80) cc_final: 0.6869 (mmm160) REVERT: K 83 LEU cc_start: 0.5292 (mt) cc_final: 0.4989 (tt) REVERT: L 25 VAL cc_start: 0.5952 (OUTLIER) cc_final: 0.5539 (m) REVERT: L 27 GLN cc_start: 0.7570 (mt0) cc_final: 0.7209 (mm-40) REVERT: P 27 ARG cc_start: 0.7394 (tpp80) cc_final: 0.6945 (tmt170) REVERT: P 38 PHE cc_start: 0.8912 (t80) cc_final: 0.8659 (t80) REVERT: P 43 ASP cc_start: 0.7495 (m-30) cc_final: 0.7078 (t0) REVERT: P 117 GLU cc_start: 0.9015 (tt0) cc_final: 0.8565 (pm20) REVERT: P 123 VAL cc_start: 0.9105 (t) cc_final: 0.8725 (m) REVERT: P 128 SER cc_start: 0.8597 (m) cc_final: 0.8227 (p) REVERT: P 135 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7523 (tp30) REVERT: P 198 MET cc_start: 0.8959 (ttm) cc_final: 0.8740 (ttp) REVERT: P 200 ASP cc_start: 0.8937 (m-30) cc_final: 0.8599 (m-30) REVERT: Q 26 ARG cc_start: 0.8488 (ptp-170) cc_final: 0.8257 (ptt-90) REVERT: Q 82 ARG cc_start: 0.8449 (mtp85) cc_final: 0.7784 (mtm-85) REVERT: Q 103 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7582 (tmm) REVERT: Q 131 ASP cc_start: 0.6222 (p0) cc_final: 0.5827 (p0) REVERT: Q 152 ARG cc_start: 0.8633 (ttt180) cc_final: 0.8291 (ttp-110) REVERT: Q 198 GLU cc_start: 0.8630 (tp30) cc_final: 0.8222 (mt-10) REVERT: R 54 GLU cc_start: 0.8466 (mp0) cc_final: 0.8222 (mp0) REVERT: R 83 ILE cc_start: 0.8400 (mm) cc_final: 0.8125 (tp) REVERT: R 176 SER cc_start: 0.9150 (m) cc_final: 0.8563 (t) REVERT: S 118 GLU cc_start: 0.9008 (tt0) cc_final: 0.8718 (tm-30) REVERT: T 2 LYS cc_start: 0.7985 (ttmt) cc_final: 0.7621 (mptt) REVERT: T 85 ARG cc_start: 0.9122 (ttp80) cc_final: 0.8823 (ttp80) REVERT: T 97 VAL cc_start: 0.8420 (t) cc_final: 0.8185 (m) REVERT: T 118 GLU cc_start: 0.7320 (pt0) cc_final: 0.6400 (mm-30) REVERT: T 150 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8276 (pp20) REVERT: T 151 ASP cc_start: 0.7430 (m-30) cc_final: 0.7137 (m-30) REVERT: T 152 ASP cc_start: 0.7529 (t0) cc_final: 0.7273 (t0) REVERT: T 201 GLN cc_start: 0.8879 (mm110) cc_final: 0.8644 (mm110) REVERT: T 203 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8368 (tm-30) REVERT: T 210 GLN cc_start: 0.7761 (mt0) cc_final: 0.7300 (mm110) REVERT: T 218 GLU cc_start: 0.8469 (pp20) cc_final: 0.8036 (mm-30) REVERT: U 16 LEU cc_start: 0.7791 (mt) cc_final: 0.7514 (tt) REVERT: U 46 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.6180 (mt) REVERT: U 72 LYS cc_start: 0.7853 (mttt) cc_final: 0.7475 (tppt) REVERT: U 95 GLU cc_start: 0.7380 (tp30) cc_final: 0.6574 (pp20) REVERT: U 158 ASP cc_start: 0.8508 (m-30) cc_final: 0.8218 (m-30) REVERT: U 167 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8585 (mm-30) REVERT: U 184 GLU cc_start: 0.7985 (tt0) cc_final: 0.7714 (tm-30) REVERT: V 46 VAL cc_start: 0.7986 (p) cc_final: 0.7778 (m) REVERT: V 77 ARG cc_start: 0.8286 (ttp-170) cc_final: 0.8068 (mtp-110) REVERT: V 153 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6966 (mt-10) REVERT: V 179 CYS cc_start: 0.9242 (t) cc_final: 0.8846 (t) REVERT: W 54 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8338 (ttm170) REVERT: W 57 ARG cc_start: 0.8535 (ttp-170) cc_final: 0.8205 (mtp180) REVERT: W 64 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7935 (mm-30) REVERT: W 72 GLU cc_start: 0.9246 (tm-30) cc_final: 0.9009 (mt-10) REVERT: W 88 GLU cc_start: 0.9335 (mp0) cc_final: 0.8650 (pp20) REVERT: X 109 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8742 (m) REVERT: X 116 ARG cc_start: 0.8928 (mtt90) cc_final: 0.8503 (tpt-90) REVERT: X 118 GLN cc_start: 0.7979 (mt0) cc_final: 0.7727 (mp10) REVERT: Y 9 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8273 (tptt) REVERT: Y 33 VAL cc_start: 0.8591 (m) cc_final: 0.8205 (p) REVERT: Y 104 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7951 (ttm170) REVERT: Y 141 TYR cc_start: 0.8766 (t80) cc_final: 0.8497 (t80) REVERT: Z 20 TYR cc_start: 0.7153 (t80) cc_final: 0.6827 (t80) REVERT: a 2 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8498 (mm-30) REVERT: a 7 GLN cc_start: 0.8370 (mt0) cc_final: 0.8099 (mp10) REVERT: a 49 GLU cc_start: 0.8781 (tp30) cc_final: 0.8477 (tp30) REVERT: b 16 ASN cc_start: 0.9255 (m-40) cc_final: 0.8877 (m-40) REVERT: b 24 GLN cc_start: 0.8924 (pm20) cc_final: 0.8549 (pm20) REVERT: b 104 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8500 (pp) REVERT: b 111 MET cc_start: 0.8974 (ptm) cc_final: 0.8723 (ptp) REVERT: b 115 GLU cc_start: 0.9103 (tt0) cc_final: 0.8716 (tm-30) REVERT: c 3 LYS cc_start: 0.8384 (mttm) cc_final: 0.7990 (mttt) REVERT: c 30 LYS cc_start: 0.8488 (tppp) cc_final: 0.8166 (mmtt) REVERT: c 55 GLU cc_start: 0.7947 (pt0) cc_final: 0.7567 (tp30) REVERT: c 99 ASN cc_start: 0.8025 (m110) cc_final: 0.7548 (t0) REVERT: c 136 TRP cc_start: 0.7889 (t60) cc_final: 0.7671 (t60) REVERT: d 18 LEU cc_start: 0.9096 (mt) cc_final: 0.8837 (mt) REVERT: d 32 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8292 (ttp80) REVERT: d 42 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8576 (tm-30) REVERT: d 63 GLN cc_start: 0.8850 (tp-100) cc_final: 0.8512 (tt0) REVERT: d 98 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8586 (pp20) REVERT: d 106 GLN cc_start: 0.8677 (pt0) cc_final: 0.8357 (mm-40) REVERT: f 6 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: f 79 PHE cc_start: 0.8123 (p90) cc_final: 0.7811 (p90) REVERT: t 121 LYS cc_start: 0.6378 (mmtt) cc_final: 0.6087 (mttt) REVERT: t 218 HIS cc_start: 0.7675 (m-70) cc_final: 0.7395 (t-90) REVERT: t 220 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.8058 (p90) REVERT: t 291 ARG cc_start: 0.7922 (mmp80) cc_final: 0.7517 (mmp80) REVERT: t 525 TRP cc_start: 0.8484 (t-100) cc_final: 0.8094 (t-100) REVERT: t 588 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8380 (mm-30) REVERT: t 617 GLN cc_start: 0.7795 (mt0) cc_final: 0.7495 (tt0) REVERT: t 638 ASN cc_start: 0.8679 (t0) cc_final: 0.8101 (t0) REVERT: t 643 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7587 (mm-30) REVERT: t 754 TYR cc_start: 0.7956 (m-10) cc_final: 0.7452 (m-80) REVERT: t 780 MET cc_start: 0.7861 (mmt) cc_final: 0.7430 (tpt) REVERT: g 26 LYS cc_start: 0.6662 (ptmt) cc_final: 0.6386 (mmtm) REVERT: g 33 ARG cc_start: 0.8544 (ttp80) cc_final: 0.8242 (ttp80) REVERT: p 124 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7159 (pp) REVERT: p 125 LYS cc_start: 0.8462 (mptt) cc_final: 0.8241 (pttt) REVERT: p 129 ARG cc_start: 0.3879 (mtp-110) cc_final: 0.3376 (tpt170) REVERT: p 196 ASP cc_start: 0.8641 (m-30) cc_final: 0.8382 (t70) REVERT: p 221 ARG cc_start: 0.6636 (mtm-85) cc_final: 0.6290 (mtp-110) REVERT: p 264 ARG cc_start: 0.6330 (mmt90) cc_final: 0.5938 (ptt180) REVERT: p 269 ARG cc_start: 0.4817 (ptt180) cc_final: 0.4403 (ttp-170) REVERT: r 9 ARG cc_start: 0.6215 (ptp-170) cc_final: 0.4392 (tpp-160) REVERT: r 65 MET cc_start: 0.2465 (mmp) cc_final: 0.1546 (ttp) outliers start: 169 outliers final: 94 residues processed: 1012 average time/residue: 0.8132 time to fit residues: 1409.7359 Evaluate side-chains 908 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 802 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 ASN Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 135 GLU Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain S residue 206 ASP Chi-restraints excluded: chain S residue 253 ASP Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 127 THR Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 179 VAL Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 166 LEU Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 173 TYR Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain V residue 153 GLU Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain Z residue 99 GLN Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain b residue 42 GLN Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain f residue 6 ASP Chi-restraints excluded: chain f residue 9 HIS Chi-restraints excluded: chain f residue 26 GLN Chi-restraints excluded: chain f residue 40 CYS Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 99 ASP Chi-restraints excluded: chain t residue 150 ASP Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 206 LEU Chi-restraints excluded: chain t residue 220 PHE Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 482 PHE Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 665 SER Chi-restraints excluded: chain t residue 735 LEU Chi-restraints excluded: chain t residue 737 THR Chi-restraints excluded: chain t residue 751 THR Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain p residue 98 LYS Chi-restraints excluded: chain p residue 124 LEU Chi-restraints excluded: chain p residue 164 LEU Chi-restraints excluded: chain p residue 192 THR Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain p residue 262 ASN Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 107 SER Chi-restraints excluded: chain r residue 250 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 220 optimal weight: 1.9990 chunk 591 optimal weight: 3.9990 chunk 129 optimal weight: 30.0000 chunk 385 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 656 optimal weight: 50.0000 chunk 545 optimal weight: 0.0970 chunk 304 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 344 optimal weight: 3.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 GLN P 23 HIS Q 49 ASN Q 92 GLN Q 99 ASN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 ASN S 157 ASN T 65 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 139 GLN ** Y 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 49 HIS ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 599 GLN ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 270 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 80787 Z= 0.305 Angle : 0.746 14.869 117118 Z= 0.379 Chirality : 0.042 0.319 14414 Planarity : 0.005 0.060 8812 Dihedral : 24.003 179.696 31550 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.57 % Favored : 88.10 % Rotamer: Outliers : 5.16 % Allowed : 19.74 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 1.35 % Twisted General : 0.36 % 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: -2.23 (0.11), residues: 5153 helix: -0.09 (0.13), residues: 1694 sheet: -1.63 (0.19), residues: 703 loop : -2.42 (0.11), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP t 778 HIS 0.012 0.001 HIS r 185 PHE 0.036 0.002 PHE r 279 TYR 0.041 0.002 TYR R 243 ARG 0.010 0.001 ARG t 502 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 814 time to evaluate : 4.418 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: D 25 GLU cc_start: 0.4389 (OUTLIER) cc_final: 0.4028 (pp20) REVERT: B 46 TRP cc_start: 0.6287 (m-90) cc_final: 0.5903 (m-10) REVERT: B 54 LYS cc_start: 0.4042 (mtpp) cc_final: 0.3598 (ptpp) REVERT: B 72 HIS cc_start: 0.7604 (t-90) cc_final: 0.7394 (t-90) REVERT: B 165 LEU cc_start: 0.7404 (tp) cc_final: 0.6655 (pp) REVERT: B 196 GLU cc_start: 0.5832 (OUTLIER) cc_final: 0.4599 (tm-30) REVERT: E 22 LEU cc_start: 0.7674 (mt) cc_final: 0.7159 (tt) REVERT: E 28 MET cc_start: 0.5044 (tmm) cc_final: 0.4801 (tmm) REVERT: E 49 MET cc_start: 0.3675 (mtp) cc_final: 0.3427 (mmp) REVERT: H 56 LYS cc_start: 0.6142 (ttmt) cc_final: 0.5571 (mmtp) REVERT: H 73 MET cc_start: 0.7754 (mtt) cc_final: 0.7548 (mmt) REVERT: I 67 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6372 (mpp) REVERT: I 134 ARG cc_start: 0.7645 (ptm-80) cc_final: 0.6824 (mmm160) REVERT: L 27 GLN cc_start: 0.7621 (mt0) cc_final: 0.7343 (mp10) REVERT: P 27 ARG cc_start: 0.7458 (tpp80) cc_final: 0.7017 (tmt170) REVERT: P 38 PHE cc_start: 0.9042 (t80) cc_final: 0.8805 (t80) REVERT: P 43 ASP cc_start: 0.7671 (m-30) cc_final: 0.7258 (t0) REVERT: P 117 GLU cc_start: 0.9063 (tt0) cc_final: 0.8638 (pm20) REVERT: P 123 VAL cc_start: 0.9271 (t) cc_final: 0.8831 (m) REVERT: P 128 SER cc_start: 0.8651 (m) cc_final: 0.8282 (p) REVERT: P 135 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: P 198 MET cc_start: 0.8952 (ttm) cc_final: 0.8711 (ttp) REVERT: P 200 ASP cc_start: 0.8946 (m-30) cc_final: 0.8561 (m-30) REVERT: Q 26 ARG cc_start: 0.8490 (ptp-170) cc_final: 0.8216 (ptt-90) REVERT: Q 30 PHE cc_start: 0.8610 (m-80) cc_final: 0.8339 (m-80) REVERT: Q 105 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: Q 131 ASP cc_start: 0.6458 (p0) cc_final: 0.6065 (p0) REVERT: Q 152 ARG cc_start: 0.8604 (ttt180) cc_final: 0.8260 (ttp-110) REVERT: R 54 GLU cc_start: 0.8567 (mp0) cc_final: 0.8261 (mp0) REVERT: R 83 ILE cc_start: 0.8514 (mm) cc_final: 0.8236 (tp) REVERT: R 88 LYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6388 (pttt) REVERT: R 120 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8784 (pt0) REVERT: R 176 SER cc_start: 0.9234 (m) cc_final: 0.8614 (t) REVERT: S 118 GLU cc_start: 0.9061 (tt0) cc_final: 0.8771 (tm-30) REVERT: S 230 GLU cc_start: 0.7593 (mp0) cc_final: 0.7030 (tm-30) REVERT: T 2 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7702 (mttp) REVERT: T 97 VAL cc_start: 0.8553 (t) cc_final: 0.8295 (m) REVERT: T 118 GLU cc_start: 0.7288 (pt0) cc_final: 0.6463 (mm-30) REVERT: T 150 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8189 (pp20) REVERT: T 151 ASP cc_start: 0.7686 (m-30) cc_final: 0.7375 (m-30) REVERT: T 201 GLN cc_start: 0.8952 (mm110) cc_final: 0.8425 (mp10) REVERT: T 203 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8330 (tm-30) REVERT: T 218 GLU cc_start: 0.8479 (pp20) cc_final: 0.8023 (mm-30) REVERT: U 16 LEU cc_start: 0.7615 (mt) cc_final: 0.7309 (tt) REVERT: U 30 SER cc_start: 0.5364 (m) cc_final: 0.4878 (t) REVERT: U 72 LYS cc_start: 0.7939 (mttt) cc_final: 0.7645 (mmmt) REVERT: U 88 ARG cc_start: 0.7285 (mmt90) cc_final: 0.6994 (mmt90) REVERT: U 95 GLU cc_start: 0.7311 (tp30) cc_final: 0.6571 (pp20) REVERT: U 158 ASP cc_start: 0.8450 (m-30) cc_final: 0.8201 (m-30) REVERT: U 164 TYR cc_start: 0.7866 (p90) cc_final: 0.7653 (p90) REVERT: U 167 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8547 (mm-30) REVERT: U 184 GLU cc_start: 0.8059 (tt0) cc_final: 0.7791 (tm-30) REVERT: V 46 VAL cc_start: 0.8484 (p) cc_final: 0.8283 (m) REVERT: V 64 ASN cc_start: 0.8695 (t0) cc_final: 0.8231 (t0) REVERT: V 77 ARG cc_start: 0.8417 (ttp-170) cc_final: 0.8182 (mtp-110) REVERT: V 153 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6966 (mt-10) REVERT: V 179 CYS cc_start: 0.9297 (t) cc_final: 0.8874 (t) REVERT: W 33 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8071 (tp30) REVERT: W 54 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8467 (ttm-80) REVERT: W 64 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8128 (mm-30) REVERT: W 88 GLU cc_start: 0.9356 (mp0) cc_final: 0.8666 (pp20) REVERT: X 22 ASN cc_start: 0.8501 (t0) cc_final: 0.8250 (t0) REVERT: X 116 ARG cc_start: 0.8893 (mtt90) cc_final: 0.8428 (tpt-90) REVERT: X 118 GLN cc_start: 0.8053 (mt0) cc_final: 0.7771 (mp10) REVERT: Y 9 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8450 (tptt) REVERT: Y 33 VAL cc_start: 0.8590 (m) cc_final: 0.8305 (p) REVERT: Y 141 TYR cc_start: 0.8761 (t80) cc_final: 0.8479 (t80) REVERT: Z 20 TYR cc_start: 0.7246 (t80) cc_final: 0.6826 (t80) REVERT: a 2 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8622 (mm-30) REVERT: a 49 GLU cc_start: 0.8865 (tp30) cc_final: 0.8623 (tp30) REVERT: b 16 ASN cc_start: 0.9365 (m-40) cc_final: 0.8964 (m-40) REVERT: b 24 GLN cc_start: 0.8978 (pm20) cc_final: 0.8598 (pm20) REVERT: b 104 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8643 (pp) REVERT: b 115 GLU cc_start: 0.9190 (tt0) cc_final: 0.8793 (tm-30) REVERT: c 30 LYS cc_start: 0.8578 (tppp) cc_final: 0.8243 (mmtt) REVERT: c 55 GLU cc_start: 0.8092 (pt0) cc_final: 0.7700 (tp30) REVERT: c 99 ASN cc_start: 0.8107 (m110) cc_final: 0.7489 (t0) REVERT: d 3 ASP cc_start: 0.4298 (t70) cc_final: 0.3928 (t70) REVERT: d 42 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8646 (tm-30) REVERT: d 63 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8478 (tt0) REVERT: d 98 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8596 (pp20) REVERT: d 106 GLN cc_start: 0.8797 (pt0) cc_final: 0.8530 (mm-40) REVERT: f 79 PHE cc_start: 0.8166 (p90) cc_final: 0.7868 (p90) REVERT: t 121 LYS cc_start: 0.6458 (mmtt) cc_final: 0.6154 (mttt) REVERT: t 218 HIS cc_start: 0.7753 (m-70) cc_final: 0.7477 (t-90) REVERT: t 291 ARG cc_start: 0.8131 (mmp80) cc_final: 0.7703 (mmp80) REVERT: t 525 TRP cc_start: 0.8567 (t-100) cc_final: 0.8181 (t-100) REVERT: t 643 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7675 (mm-30) REVERT: t 752 HIS cc_start: 0.6875 (m170) cc_final: 0.5858 (m90) REVERT: t 754 TYR cc_start: 0.7876 (m-10) cc_final: 0.7416 (m-80) REVERT: t 780 MET cc_start: 0.7833 (mmt) cc_final: 0.7419 (tpt) REVERT: g 26 LYS cc_start: 0.6654 (ptmt) cc_final: 0.6358 (mmtm) REVERT: p 124 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7123 (pp) REVERT: p 129 ARG cc_start: 0.3769 (mtp-110) cc_final: 0.3316 (tpt170) REVERT: p 196 ASP cc_start: 0.8663 (m-30) cc_final: 0.8352 (t70) REVERT: p 221 ARG cc_start: 0.6755 (mtm-85) cc_final: 0.6407 (mtp-110) REVERT: p 264 ARG cc_start: 0.6371 (mmt90) cc_final: 0.6008 (ptt180) REVERT: p 269 ARG cc_start: 0.4750 (ptt180) cc_final: 0.4315 (ttp-170) REVERT: r 65 MET cc_start: 0.2211 (OUTLIER) cc_final: 0.1664 (ttp) outliers start: 215 outliers final: 145 residues processed: 948 average time/residue: 0.7631 time to fit residues: 1246.1348 Evaluate side-chains 930 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 774 time to evaluate : 4.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 67 MET Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain N residue 106 TYR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 135 GLU Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 105 PHE Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 158 THR Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 206 ASP Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 253 ASP Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 127 THR Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 168 THR Chi-restraints excluded: chain T residue 179 VAL Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 77 LEU Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 166 LEU Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 173 TYR Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain V residue 153 GLU Chi-restraints excluded: chain V residue 188 GLU Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 100 LYS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 5 HIS Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain Z residue 99 GLN Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain b residue 42 GLN Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 9 HIS Chi-restraints excluded: chain f residue 26 GLN Chi-restraints excluded: chain f residue 37 CYS Chi-restraints excluded: chain f residue 40 CYS Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain t residue 68 ASP Chi-restraints excluded: chain t residue 70 ILE Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 99 ASP Chi-restraints excluded: chain t residue 104 LEU Chi-restraints excluded: chain t residue 148 ILE Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 206 LEU Chi-restraints excluded: chain t residue 220 PHE Chi-restraints excluded: chain t residue 277 VAL Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 568 LEU Chi-restraints excluded: chain t residue 665 SER Chi-restraints excluded: chain t residue 681 GLU Chi-restraints excluded: chain t residue 706 HIS Chi-restraints excluded: chain t residue 735 LEU Chi-restraints excluded: chain t residue 737 THR Chi-restraints excluded: chain t residue 751 THR Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain p residue 124 LEU Chi-restraints excluded: chain p residue 164 LEU Chi-restraints excluded: chain p residue 192 THR Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain p residue 250 LEU Chi-restraints excluded: chain p residue 259 VAL Chi-restraints excluded: chain p residue 262 ASN Chi-restraints excluded: chain r residue 32 VAL Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain r residue 107 SER Chi-restraints excluded: chain r residue 182 ASN Chi-restraints excluded: chain r residue 217 ILE Chi-restraints excluded: chain r residue 250 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 633 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 374 optimal weight: 5.9990 chunk 479 optimal weight: 20.0000 chunk 371 optimal weight: 10.0000 chunk 553 optimal weight: 1.9990 chunk 366 optimal weight: 9.9990 chunk 654 optimal weight: 20.0000 chunk 409 optimal weight: 6.9990 chunk 398 optimal weight: 3.9990 chunk 302 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN C 31 ASN H 103 ASN I 43 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 ASN ** P 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN Q 99 ASN R 59 HIS S 130 GLN T 65 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 599 GLN p 104 HIS ** p 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 80787 Z= 0.412 Angle : 0.849 15.953 117118 Z= 0.430 Chirality : 0.047 0.355 14414 Planarity : 0.006 0.082 8812 Dihedral : 24.161 179.584 31550 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.50 % Favored : 87.15 % Rotamer: Outliers : 5.71 % Allowed : 20.19 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 1.35 % Twisted General : 0.34 % 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: -2.46 (0.11), residues: 5153 helix: -0.36 (0.13), residues: 1693 sheet: -1.72 (0.19), residues: 685 loop : -2.52 (0.11), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP Q 29 HIS 0.019 0.002 HIS P 32 PHE 0.027 0.003 PHE I 14 TYR 0.049 0.003 TYR R 243 ARG 0.013 0.001 ARG t 502 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 832 time to evaluate : 4.480 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 TARDY: cannot create tardy model for: "SER t 772 " (corrupted residue). Skipping it. REVERT: D 25 GLU cc_start: 0.4336 (OUTLIER) cc_final: 0.3910 (pp20) REVERT: B 46 TRP cc_start: 0.6283 (m-90) cc_final: 0.5877 (m-10) REVERT: B 54 LYS cc_start: 0.4215 (mtpp) cc_final: 0.3679 (ptpp) REVERT: B 66 GLN cc_start: 0.5350 (OUTLIER) cc_final: 0.5126 (mp10) REVERT: B 149 VAL cc_start: 0.6370 (OUTLIER) cc_final: 0.5969 (m) REVERT: B 165 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6680 (pp) REVERT: B 196 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.4574 (tm-30) REVERT: E 28 MET cc_start: 0.5435 (tmm) cc_final: 0.5216 (tmm) REVERT: E 80 MET cc_start: 0.5931 (ttt) cc_final: 0.5419 (ptm) REVERT: H 56 LYS cc_start: 0.5884 (ttmt) cc_final: 0.5365 (mmtp) REVERT: H 119 ILE cc_start: 0.3095 (OUTLIER) cc_final: 0.2676 (tp) REVERT: I 130 ARG cc_start: 0.6704 (tpp80) cc_final: 0.6263 (tmt-80) REVERT: I 134 ARG cc_start: 0.7699 (ptm-80) cc_final: 0.6928 (tpp-160) REVERT: L 27 GLN cc_start: 0.7581 (mt0) cc_final: 0.7091 (mm-40) REVERT: P 27 ARG cc_start: 0.7521 (tpp80) cc_final: 0.7060 (tmt170) REVERT: P 38 PHE cc_start: 0.9121 (t80) cc_final: 0.8827 (t80) REVERT: P 43 ASP cc_start: 0.8045 (m-30) cc_final: 0.7620 (t0) REVERT: P 55 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: P 117 GLU cc_start: 0.9040 (tt0) cc_final: 0.8640 (pm20) REVERT: P 128 SER cc_start: 0.8662 (m) cc_final: 0.8311 (p) REVERT: P 135 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: P 200 ASP cc_start: 0.9128 (m-30) cc_final: 0.8875 (m-30) REVERT: Q 26 ARG cc_start: 0.8251 (ptp-170) cc_final: 0.7999 (ptt-90) REVERT: Q 64 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7652 (ptm160) REVERT: Q 105 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: Q 131 ASP cc_start: 0.6508 (p0) cc_final: 0.6062 (p0) REVERT: Q 152 ARG cc_start: 0.8620 (ttt180) cc_final: 0.8239 (ttp-110) REVERT: Q 174 LYS cc_start: 0.8093 (pttp) cc_final: 0.7834 (mttp) REVERT: R 83 ILE cc_start: 0.8579 (mm) cc_final: 0.8340 (tp) REVERT: R 88 LYS cc_start: 0.6524 (OUTLIER) cc_final: 0.6098 (pttt) REVERT: R 120 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8874 (pt0) REVERT: R 176 SER cc_start: 0.9311 (m) cc_final: 0.8705 (t) REVERT: S 87 MET cc_start: 0.8842 (tpp) cc_final: 0.8431 (tpp) REVERT: S 118 GLU cc_start: 0.9132 (tt0) cc_final: 0.8842 (tm-30) REVERT: S 230 GLU cc_start: 0.7613 (mp0) cc_final: 0.7018 (tm-30) REVERT: T 2 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7692 (mttp) REVERT: T 97 VAL cc_start: 0.8613 (t) cc_final: 0.8334 (m) REVERT: T 150 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8194 (pp20) REVERT: T 151 ASP cc_start: 0.7829 (m-30) cc_final: 0.7400 (m-30) REVERT: T 201 GLN cc_start: 0.9020 (mm110) cc_final: 0.8532 (mp10) REVERT: T 203 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8351 (tm-30) REVERT: U 16 LEU cc_start: 0.7726 (mt) cc_final: 0.7433 (tt) REVERT: U 30 SER cc_start: 0.5609 (m) cc_final: 0.5186 (t) REVERT: U 46 ILE cc_start: 0.6460 (OUTLIER) cc_final: 0.5250 (mt) REVERT: U 60 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8353 (tp) REVERT: U 72 LYS cc_start: 0.8046 (mttt) cc_final: 0.7800 (mmmt) REVERT: U 95 GLU cc_start: 0.7563 (tp30) cc_final: 0.6756 (pp20) REVERT: U 158 ASP cc_start: 0.8364 (m-30) cc_final: 0.8115 (m-30) REVERT: U 167 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8580 (mm-30) REVERT: V 46 VAL cc_start: 0.8655 (p) cc_final: 0.8412 (m) REVERT: V 77 ARG cc_start: 0.8507 (ttp-170) cc_final: 0.8301 (mtp-110) REVERT: V 153 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7180 (mt-10) REVERT: V 179 CYS cc_start: 0.9286 (t) cc_final: 0.8949 (t) REVERT: W 13 SER cc_start: 0.9159 (t) cc_final: 0.8820 (p) REVERT: W 33 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8178 (tp30) REVERT: W 64 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8195 (mm-30) REVERT: W 88 GLU cc_start: 0.9363 (mp0) cc_final: 0.8709 (pp20) REVERT: X 22 ASN cc_start: 0.8529 (t0) cc_final: 0.8291 (t0) REVERT: X 116 ARG cc_start: 0.8866 (mtt90) cc_final: 0.8400 (tpt-90) REVERT: X 118 GLN cc_start: 0.8124 (mt0) cc_final: 0.7885 (mp10) REVERT: Y 9 LYS cc_start: 0.9209 (mmtt) cc_final: 0.8507 (tptt) REVERT: Y 33 VAL cc_start: 0.8606 (m) cc_final: 0.8311 (p) REVERT: Y 141 TYR cc_start: 0.8816 (t80) cc_final: 0.8450 (t80) REVERT: a 2 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8636 (mm-30) REVERT: a 49 GLU cc_start: 0.8938 (tp30) cc_final: 0.8490 (tp30) REVERT: b 12 ASN cc_start: 0.9122 (t0) cc_final: 0.8776 (t0) REVERT: b 16 ASN cc_start: 0.9363 (m-40) cc_final: 0.8996 (m-40) REVERT: b 24 GLN cc_start: 0.9023 (pm20) cc_final: 0.8701 (pm20) REVERT: b 104 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8753 (pp) REVERT: b 115 GLU cc_start: 0.9248 (tt0) cc_final: 0.8827 (tm-30) REVERT: c 30 LYS cc_start: 0.8595 (tppp) cc_final: 0.8249 (mmtt) REVERT: c 34 LEU cc_start: 0.8697 (mm) cc_final: 0.8108 (tp) REVERT: c 55 GLU cc_start: 0.8130 (pt0) cc_final: 0.7763 (tp30) REVERT: c 99 ASN cc_start: 0.7964 (m110) cc_final: 0.7429 (t0) REVERT: d 3 ASP cc_start: 0.4822 (t70) cc_final: 0.4512 (t70) REVERT: d 18 LEU cc_start: 0.9214 (mt) cc_final: 0.8912 (mt) REVERT: d 42 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8676 (tm-30) REVERT: d 63 GLN cc_start: 0.9045 (tp-100) cc_final: 0.8567 (tt0) REVERT: d 98 GLU cc_start: 0.9353 (mm-30) cc_final: 0.8695 (pp20) REVERT: d 106 GLN cc_start: 0.8904 (pt0) cc_final: 0.8647 (mm-40) REVERT: f 79 PHE cc_start: 0.8104 (p90) cc_final: 0.7813 (p90) REVERT: t 121 LYS cc_start: 0.6491 (mmtt) cc_final: 0.6149 (mttt) REVERT: t 218 HIS cc_start: 0.7734 (m-70) cc_final: 0.7493 (t-170) REVERT: t 525 TRP cc_start: 0.8633 (t-100) cc_final: 0.8269 (t-100) REVERT: t 588 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8550 (mm-30) REVERT: t 599 GLN cc_start: 0.8700 (tt0) cc_final: 0.8444 (mt0) REVERT: t 623 TYR cc_start: 0.8292 (m-10) cc_final: 0.8037 (m-10) REVERT: t 643 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7675 (mm-30) REVERT: t 679 ASN cc_start: 0.8376 (t0) cc_final: 0.8128 (t0) REVERT: t 752 HIS cc_start: 0.6749 (m170) cc_final: 0.5624 (m90) REVERT: t 754 TYR cc_start: 0.7918 (m-10) cc_final: 0.7476 (m-80) REVERT: t 780 MET cc_start: 0.7920 (mmt) cc_final: 0.7520 (tpt) REVERT: g 26 LYS cc_start: 0.6675 (ptmt) cc_final: 0.6362 (mmtm) REVERT: p 188 LYS cc_start: 0.8546 (mtmp) cc_final: 0.8162 (tptp) REVERT: p 196 ASP cc_start: 0.8673 (m-30) cc_final: 0.8373 (t70) REVERT: p 221 ARG cc_start: 0.6838 (mtm-85) cc_final: 0.6510 (mtp-110) REVERT: p 264 ARG cc_start: 0.6329 (mmt90) cc_final: 0.5947 (ptt180) REVERT: p 269 ARG cc_start: 0.4945 (ptt180) cc_final: 0.4476 (ttp-170) REVERT: r 65 MET cc_start: 0.2268 (OUTLIER) cc_final: 0.1667 (ttp) outliers start: 238 outliers final: 168 residues processed: 982 average time/residue: 0.7237 time to fit residues: 1218.2839 Evaluate side-chains 954 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 770 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 61 TYR Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 ASN Chi-restraints excluded: chain N residue 106 TYR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 135 GLU Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 105 PHE Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 158 THR Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 206 ASP Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 253 ASP Chi-restraints excluded: chain T residue 13 GLN Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 127 THR Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 168 THR Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain U residue 77 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 166 LEU Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 173 TYR Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 94 ASN Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain V residue 153 GLU Chi-restraints excluded: chain V residue 188 GLU Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 100 LYS Chi-restraints excluded: chain W residue 105 LEU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 49 ILE Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 5 HIS Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Z residue 14 PHE Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 99 GLN Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 42 GLN Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 83 ILE Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 98 GLU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 128 SER Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 9 HIS Chi-restraints excluded: chain f residue 26 GLN Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 37 CYS Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 78 SER Chi-restraints excluded: chain t residue 70 ILE Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 99 ASP Chi-restraints excluded: chain t residue 104 LEU Chi-restraints excluded: chain t residue 113 ILE Chi-restraints excluded: chain t residue 148 ILE Chi-restraints excluded: chain t residue 150 ASP Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 206 LEU Chi-restraints excluded: chain t residue 208 VAL Chi-restraints excluded: chain t residue 220 PHE Chi-restraints excluded: chain t residue 254 ASP Chi-restraints excluded: chain t residue 277 VAL Chi-restraints excluded: chain t residue 336 VAL Chi-restraints excluded: chain t residue 482 PHE Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 545 THR Chi-restraints excluded: chain t residue 657 ILE Chi-restraints excluded: chain t residue 665 SER Chi-restraints excluded: chain t residue 681 GLU Chi-restraints excluded: chain t residue 706 HIS Chi-restraints excluded: chain t residue 733 ILE Chi-restraints excluded: chain t residue 737 THR Chi-restraints excluded: chain t residue 751 THR Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 56 MET Chi-restraints excluded: chain p residue 192 THR Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain p residue 239 HIS Chi-restraints excluded: chain p residue 250 LEU Chi-restraints excluded: chain p residue 259 VAL Chi-restraints excluded: chain p residue 262 ASN Chi-restraints excluded: chain r residue 32 VAL Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain r residue 107 SER Chi-restraints excluded: chain r residue 121 VAL Chi-restraints excluded: chain r residue 155 SER Chi-restraints excluded: chain r residue 182 ASN Chi-restraints excluded: chain r residue 185 HIS Chi-restraints excluded: chain r residue 217 ILE Chi-restraints excluded: chain r residue 250 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 404 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 390 optimal weight: 7.9990 chunk 197 optimal weight: 0.0070 chunk 128 optimal weight: 30.0000 chunk 126 optimal weight: 40.0000 chunk 416 optimal weight: 0.8980 chunk 445 optimal weight: 0.0970 chunk 323 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 514 optimal weight: 4.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS H 104 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN ** P 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 GLN Q 99 ASN Q 208 GLN Q 232 HIS R 152 HIS S 130 GLN T 65 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 HIS ** Y 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 509 ASN t 550 GLN ** t 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 234 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 80787 Z= 0.185 Angle : 0.688 14.870 117118 Z= 0.351 Chirality : 0.040 0.336 14414 Planarity : 0.005 0.061 8812 Dihedral : 23.903 179.137 31548 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.79 % Favored : 89.00 % Rotamer: Outliers : 3.88 % Allowed : 22.47 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 0.90 % Twisted General : 0.30 % 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: -2.11 (0.12), residues: 5153 helix: 0.00 (0.13), residues: 1713 sheet: -1.52 (0.19), residues: 681 loop : -2.37 (0.11), residues: 2759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Q 117 HIS 0.014 0.001 HIS P 32 PHE 0.027 0.002 PHE U 131 TYR 0.032 0.002 TYR R 243 ARG 0.010 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 837 time to evaluate : 4.588 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 TARDY: cannot create tardy model for: "SER t 772 " (corrupted residue). Skipping it. REVERT: D 25 GLU cc_start: 0.4136 (OUTLIER) cc_final: 0.3795 (pp20) REVERT: B 46 TRP cc_start: 0.6242 (m-90) cc_final: 0.5840 (m-10) REVERT: B 54 LYS cc_start: 0.4131 (mtpp) cc_final: 0.3734 (ptpp) REVERT: B 165 LEU cc_start: 0.7325 (tp) cc_final: 0.6644 (pp) REVERT: B 217 LEU cc_start: 0.7879 (mt) cc_final: 0.7566 (tp) REVERT: E 28 MET cc_start: 0.5543 (tmm) cc_final: 0.5170 (tmm) REVERT: H 56 LYS cc_start: 0.6109 (ttmt) cc_final: 0.5566 (mmtp) REVERT: I 7 ARG cc_start: 0.6391 (mmt90) cc_final: 0.5987 (mtt-85) REVERT: I 35 ASP cc_start: 0.2655 (OUTLIER) cc_final: 0.2384 (p0) REVERT: I 130 ARG cc_start: 0.7111 (tpp80) cc_final: 0.6647 (tmt-80) REVERT: I 134 ARG cc_start: 0.7881 (ptm-80) cc_final: 0.7131 (tpp-160) REVERT: L 27 GLN cc_start: 0.7551 (mt0) cc_final: 0.7299 (mp10) REVERT: P 7 PHE cc_start: 0.8011 (m-80) cc_final: 0.7665 (m-10) REVERT: P 27 ARG cc_start: 0.7495 (tpp80) cc_final: 0.7006 (tmt170) REVERT: P 38 PHE cc_start: 0.9042 (t80) cc_final: 0.8723 (t80) REVERT: P 43 ASP cc_start: 0.7649 (m-30) cc_final: 0.7191 (t0) REVERT: P 117 GLU cc_start: 0.9011 (tt0) cc_final: 0.8630 (pm20) REVERT: P 123 VAL cc_start: 0.9006 (t) cc_final: 0.8594 (m) REVERT: P 128 SER cc_start: 0.8595 (m) cc_final: 0.8267 (p) REVERT: P 135 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: Q 24 PHE cc_start: 0.7040 (m-10) cc_final: 0.6707 (t80) REVERT: Q 26 ARG cc_start: 0.8358 (ptp-170) cc_final: 0.8049 (ptt-90) REVERT: Q 30 PHE cc_start: 0.8768 (m-80) cc_final: 0.8464 (m-80) REVERT: Q 131 ASP cc_start: 0.5998 (p0) cc_final: 0.5517 (p0) REVERT: Q 152 ARG cc_start: 0.8550 (ttt180) cc_final: 0.8174 (ttp-110) REVERT: Q 177 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: R 83 ILE cc_start: 0.8410 (mm) cc_final: 0.8176 (tp) REVERT: R 88 LYS cc_start: 0.6554 (OUTLIER) cc_final: 0.6088 (pttt) REVERT: R 120 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8731 (pt0) REVERT: R 176 SER cc_start: 0.9235 (m) cc_final: 0.8672 (t) REVERT: S 87 MET cc_start: 0.8893 (tpp) cc_final: 0.8439 (tpp) REVERT: S 118 GLU cc_start: 0.9063 (tt0) cc_final: 0.8820 (tm-30) REVERT: T 2 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7697 (mttp) REVERT: T 97 VAL cc_start: 0.8548 (t) cc_final: 0.8234 (m) REVERT: T 150 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8154 (pp20) REVERT: T 151 ASP cc_start: 0.7650 (m-30) cc_final: 0.7232 (m-30) REVERT: T 201 GLN cc_start: 0.8937 (mm110) cc_final: 0.8439 (mp10) REVERT: T 203 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8369 (tm-30) REVERT: T 210 GLN cc_start: 0.7811 (mt0) cc_final: 0.7358 (mm110) REVERT: T 218 GLU cc_start: 0.8477 (pp20) cc_final: 0.8042 (mm-30) REVERT: U 16 LEU cc_start: 0.7721 (mt) cc_final: 0.7361 (tt) REVERT: U 28 GLU cc_start: 0.7891 (mt-10) cc_final: 0.6983 (tp30) REVERT: U 30 SER cc_start: 0.5480 (m) cc_final: 0.5108 (t) REVERT: U 72 LYS cc_start: 0.7961 (mttt) cc_final: 0.7690 (mmmt) REVERT: U 95 GLU cc_start: 0.7290 (tp30) cc_final: 0.6460 (pp20) REVERT: U 158 ASP cc_start: 0.8301 (m-30) cc_final: 0.7984 (m-30) REVERT: U 164 TYR cc_start: 0.7981 (p90) cc_final: 0.7777 (p90) REVERT: U 167 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8506 (mm-30) REVERT: U 184 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8133 (tm-30) REVERT: V 29 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8552 (pt) REVERT: V 46 VAL cc_start: 0.8378 (p) cc_final: 0.8161 (m) REVERT: V 77 ARG cc_start: 0.8405 (ttp-170) cc_final: 0.8201 (mtp-110) REVERT: V 153 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7048 (mt-10) REVERT: V 179 CYS cc_start: 0.9330 (t) cc_final: 0.8903 (t) REVERT: W 33 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8105 (tp30) REVERT: W 57 ARG cc_start: 0.8692 (ttp-170) cc_final: 0.8269 (mtp180) REVERT: W 64 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8102 (mm-30) REVERT: W 88 GLU cc_start: 0.9380 (mp0) cc_final: 0.8747 (pp20) REVERT: X 22 ASN cc_start: 0.8471 (t0) cc_final: 0.8232 (t0) REVERT: X 116 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8457 (tpt-90) REVERT: X 118 GLN cc_start: 0.8034 (mt0) cc_final: 0.7834 (mp10) REVERT: Y 9 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8401 (tptt) REVERT: Y 33 VAL cc_start: 0.8590 (m) cc_final: 0.8263 (p) REVERT: Z 20 TYR cc_start: 0.7058 (t80) cc_final: 0.6806 (t80) REVERT: a 2 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8518 (mm-30) REVERT: a 49 GLU cc_start: 0.8862 (tp30) cc_final: 0.8473 (tp30) REVERT: b 24 GLN cc_start: 0.8964 (pm20) cc_final: 0.8688 (pm20) REVERT: b 104 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8638 (pp) REVERT: b 115 GLU cc_start: 0.9112 (tt0) cc_final: 0.8736 (tm-30) REVERT: c 55 GLU cc_start: 0.8082 (pt0) cc_final: 0.7739 (tp30) REVERT: c 99 ASN cc_start: 0.8086 (m110) cc_final: 0.7570 (t0) REVERT: d 18 LEU cc_start: 0.9219 (mt) cc_final: 0.8967 (mt) REVERT: d 42 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8645 (tm-30) REVERT: d 63 GLN cc_start: 0.8955 (tp-100) cc_final: 0.8621 (tt0) REVERT: d 98 GLU cc_start: 0.9359 (mm-30) cc_final: 0.8653 (pp20) REVERT: d 106 GLN cc_start: 0.8714 (pt0) cc_final: 0.8490 (mm-40) REVERT: f 29 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7818 (mtt-85) REVERT: f 79 PHE cc_start: 0.8084 (p90) cc_final: 0.7806 (p90) REVERT: t 121 LYS cc_start: 0.6435 (mmtt) cc_final: 0.6128 (mttt) REVERT: t 524 GLU cc_start: 0.8607 (mp0) cc_final: 0.8393 (mp0) REVERT: t 525 TRP cc_start: 0.8471 (t-100) cc_final: 0.8070 (t-100) REVERT: t 588 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8515 (mm-30) REVERT: t 599 GLN cc_start: 0.8391 (tt0) cc_final: 0.8148 (mt0) REVERT: t 623 TYR cc_start: 0.8197 (m-10) cc_final: 0.7749 (m-10) REVERT: t 720 MET cc_start: 0.7070 (mmm) cc_final: 0.6727 (mmm) REVERT: t 735 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7394 (tp) REVERT: t 752 HIS cc_start: 0.6955 (m170) cc_final: 0.5856 (m90) REVERT: t 754 TYR cc_start: 0.7738 (m-10) cc_final: 0.7341 (m-80) REVERT: t 780 MET cc_start: 0.7984 (mmt) cc_final: 0.7531 (tpt) REVERT: g 26 LYS cc_start: 0.6608 (ptmt) cc_final: 0.6321 (mmtm) REVERT: p 196 ASP cc_start: 0.8614 (m-30) cc_final: 0.8358 (t70) REVERT: p 221 ARG cc_start: 0.6745 (mtm-85) cc_final: 0.6383 (mtp-110) REVERT: p 264 ARG cc_start: 0.6318 (mmt90) cc_final: 0.5892 (ptt180) REVERT: p 269 ARG cc_start: 0.4533 (ptt180) cc_final: 0.4100 (ttp-170) REVERT: r 65 MET cc_start: 0.2372 (OUTLIER) cc_final: 0.1420 (ttp) REVERT: r 214 MET cc_start: 0.5497 (OUTLIER) cc_final: 0.5044 (tmm) outliers start: 162 outliers final: 113 residues processed: 935 average time/residue: 0.7267 time to fit residues: 1158.6954 Evaluate side-chains 930 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 804 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 43 ASN Chi-restraints excluded: chain N residue 106 TYR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 135 GLU Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 177 GLN Chi-restraints excluded: chain Q residue 209 ASN Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain S residue 206 ASP Chi-restraints excluded: chain S residue 253 ASP Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 127 THR Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 168 THR Chi-restraints excluded: chain T residue 179 VAL Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 166 LEU Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 173 TYR Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 153 GLU Chi-restraints excluded: chain V residue 188 GLU Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 100 LYS Chi-restraints excluded: chain X residue 18 HIS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 99 GLN Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain b residue 42 GLN Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 128 SER Chi-restraints excluded: chain d residue 17 LEU Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 26 GLN Chi-restraints excluded: chain f residue 29 ARG Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 37 CYS Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 99 ASP Chi-restraints excluded: chain t residue 113 ILE Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 206 LEU Chi-restraints excluded: chain t residue 208 VAL Chi-restraints excluded: chain t residue 220 PHE Chi-restraints excluded: chain t residue 277 VAL Chi-restraints excluded: chain t residue 482 PHE Chi-restraints excluded: chain t residue 545 THR Chi-restraints excluded: chain t residue 665 SER Chi-restraints excluded: chain t residue 735 LEU Chi-restraints excluded: chain t residue 737 THR Chi-restraints excluded: chain t residue 751 THR Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 56 MET Chi-restraints excluded: chain p residue 164 LEU Chi-restraints excluded: chain p residue 192 THR Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain p residue 239 HIS Chi-restraints excluded: chain p residue 262 ASN Chi-restraints excluded: chain r residue 32 VAL Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain r residue 107 SER Chi-restraints excluded: chain r residue 121 VAL Chi-restraints excluded: chain r residue 125 HIS Chi-restraints excluded: chain r residue 182 ASN Chi-restraints excluded: chain r residue 214 MET Chi-restraints excluded: chain r residue 250 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 595 optimal weight: 7.9990 chunk 626 optimal weight: 5.9990 chunk 572 optimal weight: 7.9990 chunk 609 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 chunk 478 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 551 optimal weight: 3.9990 chunk 576 optimal weight: 0.9990 chunk 607 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS I 43 ASN L 43 ASN ** P 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 ASN Q 208 GLN Q 232 HIS S 130 GLN T 65 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 HIS ** Y 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN b 16 ASN ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 29 HIS ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 617 GLN ** p 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 234 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 80787 Z= 0.224 Angle : 0.701 14.713 117118 Z= 0.358 Chirality : 0.040 0.409 14414 Planarity : 0.005 0.062 8812 Dihedral : 23.828 179.435 31546 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.35 % Favored : 88.41 % Rotamer: Outliers : 3.91 % Allowed : 22.69 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 0.90 % Twisted General : 0.28 % 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: -2.04 (0.12), residues: 5153 helix: 0.10 (0.13), residues: 1705 sheet: -1.53 (0.19), residues: 688 loop : -2.34 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP t 778 HIS 0.014 0.001 HIS P 32 PHE 0.028 0.002 PHE I 14 TYR 0.056 0.002 TYR R 243 ARG 0.009 0.001 ARG R 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 821 time to evaluate : 4.460 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 TARDY: cannot create tardy model for: "SER t 772 " (corrupted residue). Skipping it. REVERT: D 25 GLU cc_start: 0.4129 (OUTLIER) cc_final: 0.3772 (pp20) REVERT: B 46 TRP cc_start: 0.6272 (m-90) cc_final: 0.5803 (m-10) REVERT: B 54 LYS cc_start: 0.3867 (mtpp) cc_final: 0.3410 (ptpp) REVERT: B 165 LEU cc_start: 0.7405 (tp) cc_final: 0.6645 (pp) REVERT: C 45 ARG cc_start: 0.3921 (mmm160) cc_final: 0.2930 (mmm-85) REVERT: E 28 MET cc_start: 0.5251 (tmm) cc_final: 0.4809 (tmm) REVERT: E 111 MET cc_start: 0.5421 (mmp) cc_final: 0.4997 (mmp) REVERT: H 56 LYS cc_start: 0.6106 (ttmt) cc_final: 0.5606 (mptp) REVERT: H 119 ILE cc_start: 0.3256 (OUTLIER) cc_final: 0.2730 (tp) REVERT: I 35 ASP cc_start: 0.2519 (OUTLIER) cc_final: 0.2249 (p0) REVERT: I 67 MET cc_start: 0.7366 (mpp) cc_final: 0.6622 (mpp) REVERT: I 130 ARG cc_start: 0.7138 (tpp80) cc_final: 0.6635 (tmt-80) REVERT: I 134 ARG cc_start: 0.7908 (ptm-80) cc_final: 0.7164 (tpp-160) REVERT: L 27 GLN cc_start: 0.7396 (mt0) cc_final: 0.7095 (mp10) REVERT: P 7 PHE cc_start: 0.8002 (m-80) cc_final: 0.7670 (m-10) REVERT: P 27 ARG cc_start: 0.7466 (tpp80) cc_final: 0.6928 (tmt170) REVERT: P 38 PHE cc_start: 0.9013 (t80) cc_final: 0.8713 (t80) REVERT: P 43 ASP cc_start: 0.7676 (m-30) cc_final: 0.7204 (t0) REVERT: P 117 GLU cc_start: 0.9030 (tt0) cc_final: 0.8655 (pm20) REVERT: P 128 SER cc_start: 0.8587 (m) cc_final: 0.8278 (p) REVERT: P 135 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: Q 24 PHE cc_start: 0.7038 (m-10) cc_final: 0.6629 (t80) REVERT: Q 26 ARG cc_start: 0.8209 (ptp-170) cc_final: 0.7915 (ptt-90) REVERT: Q 30 PHE cc_start: 0.8809 (m-80) cc_final: 0.8509 (m-80) REVERT: Q 64 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7665 (ptm160) REVERT: Q 78 ASP cc_start: 0.7351 (p0) cc_final: 0.7103 (p0) REVERT: Q 131 ASP cc_start: 0.5969 (p0) cc_final: 0.5728 (p0) REVERT: Q 152 ARG cc_start: 0.8571 (ttt180) cc_final: 0.8169 (ttp-110) REVERT: Q 177 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8001 (pm20) REVERT: Q 223 PHE cc_start: 0.6114 (t80) cc_final: 0.5888 (t80) REVERT: R 83 ILE cc_start: 0.8425 (mm) cc_final: 0.8213 (tp) REVERT: R 88 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6109 (pttt) REVERT: R 120 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8674 (pt0) REVERT: R 176 SER cc_start: 0.9248 (m) cc_final: 0.8647 (t) REVERT: S 87 MET cc_start: 0.8908 (tpp) cc_final: 0.8426 (tpp) REVERT: S 118 GLU cc_start: 0.9080 (tt0) cc_final: 0.8817 (tm-30) REVERT: T 2 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7631 (mttp) REVERT: T 97 VAL cc_start: 0.8605 (t) cc_final: 0.8280 (m) REVERT: T 150 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8204 (pp20) REVERT: T 151 ASP cc_start: 0.7591 (m-30) cc_final: 0.7103 (m-30) REVERT: T 201 GLN cc_start: 0.8904 (mm110) cc_final: 0.8425 (mp10) REVERT: T 203 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8358 (tm-30) REVERT: T 210 GLN cc_start: 0.7894 (mt0) cc_final: 0.7451 (mm110) REVERT: T 218 GLU cc_start: 0.8472 (pp20) cc_final: 0.8031 (mm-30) REVERT: U 16 LEU cc_start: 0.7738 (mt) cc_final: 0.7419 (tt) REVERT: U 28 GLU cc_start: 0.7863 (mt-10) cc_final: 0.6848 (mm-30) REVERT: U 30 SER cc_start: 0.5636 (m) cc_final: 0.5214 (t) REVERT: U 72 LYS cc_start: 0.7979 (mttt) cc_final: 0.7710 (mmmt) REVERT: U 95 GLU cc_start: 0.7245 (tp30) cc_final: 0.6433 (pp20) REVERT: U 158 ASP cc_start: 0.8377 (m-30) cc_final: 0.8117 (m-30) REVERT: U 164 TYR cc_start: 0.7885 (p90) cc_final: 0.7665 (p90) REVERT: U 167 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8481 (mm-30) REVERT: U 184 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8175 (tm-30) REVERT: V 29 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8600 (pt) REVERT: V 46 VAL cc_start: 0.8424 (p) cc_final: 0.8202 (m) REVERT: V 77 ARG cc_start: 0.8383 (ttp-170) cc_final: 0.8172 (mtp-110) REVERT: V 153 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: V 179 CYS cc_start: 0.9318 (t) cc_final: 0.8903 (t) REVERT: W 57 ARG cc_start: 0.8619 (ttp-170) cc_final: 0.8286 (mtp180) REVERT: W 64 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8119 (mm-30) REVERT: W 88 GLU cc_start: 0.9368 (mp0) cc_final: 0.8705 (pp20) REVERT: X 116 ARG cc_start: 0.8900 (mtt90) cc_final: 0.8449 (tpt-90) REVERT: X 118 GLN cc_start: 0.8074 (mt0) cc_final: 0.7864 (mp10) REVERT: Y 9 LYS cc_start: 0.9112 (mmtt) cc_final: 0.8438 (tptt) REVERT: Y 33 VAL cc_start: 0.8560 (m) cc_final: 0.8263 (p) REVERT: Z 20 TYR cc_start: 0.7198 (t80) cc_final: 0.6940 (t80) REVERT: a 2 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8580 (mm-30) REVERT: a 49 GLU cc_start: 0.8887 (tp30) cc_final: 0.8460 (tp30) REVERT: b 104 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8656 (pp) REVERT: b 115 GLU cc_start: 0.9128 (tt0) cc_final: 0.8734 (tm-30) REVERT: c 55 GLU cc_start: 0.8087 (pt0) cc_final: 0.7749 (tp30) REVERT: c 99 ASN cc_start: 0.7973 (m110) cc_final: 0.7454 (t0) REVERT: d 42 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8634 (tm-30) REVERT: d 63 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8559 (tt0) REVERT: d 98 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8670 (pp20) REVERT: d 106 GLN cc_start: 0.8731 (pt0) cc_final: 0.8514 (mm-40) REVERT: f 29 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7837 (mtt-85) REVERT: f 62 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.6999 (mt) REVERT: f 79 PHE cc_start: 0.8068 (p90) cc_final: 0.7798 (p90) REVERT: t 121 LYS cc_start: 0.6456 (mmtt) cc_final: 0.6165 (mttt) REVERT: t 291 ARG cc_start: 0.8227 (mmp80) cc_final: 0.7879 (mmp80) REVERT: t 525 TRP cc_start: 0.8627 (t-100) cc_final: 0.8257 (t-100) REVERT: t 588 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8605 (mm-30) REVERT: t 599 GLN cc_start: 0.8501 (tt0) cc_final: 0.8247 (mt0) REVERT: t 623 TYR cc_start: 0.8160 (m-10) cc_final: 0.7669 (m-10) REVERT: t 720 MET cc_start: 0.7103 (mmm) cc_final: 0.6864 (mmm) REVERT: t 752 HIS cc_start: 0.6963 (m170) cc_final: 0.5812 (m90) REVERT: t 754 TYR cc_start: 0.7689 (m-10) cc_final: 0.7233 (m-80) REVERT: t 780 MET cc_start: 0.7988 (mmt) cc_final: 0.7548 (tpt) REVERT: g 26 LYS cc_start: 0.6611 (ptmt) cc_final: 0.6331 (mmtm) REVERT: p 196 ASP cc_start: 0.8600 (m-30) cc_final: 0.8326 (t70) REVERT: p 221 ARG cc_start: 0.6738 (mtm-85) cc_final: 0.6387 (mtp-110) REVERT: p 264 ARG cc_start: 0.6299 (mmt90) cc_final: 0.5867 (ptt180) REVERT: p 269 ARG cc_start: 0.4561 (ptt180) cc_final: 0.4105 (ttp-170) REVERT: r 65 MET cc_start: 0.2246 (OUTLIER) cc_final: 0.1596 (ttp) REVERT: r 214 MET cc_start: 0.5156 (OUTLIER) cc_final: 0.4734 (ptt) outliers start: 163 outliers final: 122 residues processed: 927 average time/residue: 0.7207 time to fit residues: 1136.9202 Evaluate side-chains 920 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 785 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 61 TYR Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 43 ASN Chi-restraints excluded: chain N residue 106 TYR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 135 GLU Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 177 GLN Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 206 ASP Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 253 ASP Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 127 THR Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 168 THR Chi-restraints excluded: chain T residue 179 VAL Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 77 LEU Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 166 LEU Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 173 TYR Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 153 GLU Chi-restraints excluded: chain V residue 188 GLU Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 100 LYS Chi-restraints excluded: chain X residue 18 HIS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 5 HIS Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Y residue 83 GLU Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 75 ASN Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 42 GLN Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 87 GLU Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 128 SER Chi-restraints excluded: chain d residue 14 SER Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 26 GLN Chi-restraints excluded: chain f residue 29 ARG Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 37 CYS Chi-restraints excluded: chain f residue 40 CYS Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 78 SER Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 99 ASP Chi-restraints excluded: chain t residue 104 LEU Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 206 LEU Chi-restraints excluded: chain t residue 208 VAL Chi-restraints excluded: chain t residue 220 PHE Chi-restraints excluded: chain t residue 277 VAL Chi-restraints excluded: chain t residue 482 PHE Chi-restraints excluded: chain t residue 545 THR Chi-restraints excluded: chain t residue 665 SER Chi-restraints excluded: chain t residue 706 HIS Chi-restraints excluded: chain t residue 737 THR Chi-restraints excluded: chain t residue 751 THR Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 56 MET Chi-restraints excluded: chain p residue 164 LEU Chi-restraints excluded: chain p residue 192 THR Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain p residue 262 ASN Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain r residue 107 SER Chi-restraints excluded: chain r residue 121 VAL Chi-restraints excluded: chain r residue 182 ASN Chi-restraints excluded: chain r residue 214 MET Chi-restraints excluded: chain r residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 400 optimal weight: 9.9990 chunk 644 optimal weight: 2.9990 chunk 393 optimal weight: 6.9990 chunk 305 optimal weight: 0.8980 chunk 448 optimal weight: 0.3980 chunk 676 optimal weight: 40.0000 chunk 622 optimal weight: 0.7980 chunk 538 optimal weight: 0.1980 chunk 55 optimal weight: 10.0000 chunk 416 optimal weight: 3.9990 chunk 330 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS I 43 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 118 GLN Q 232 HIS ** R 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN T 65 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 139 GLN X 18 HIS ** Y 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 617 GLN p 239 HIS r 234 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 80787 Z= 0.163 Angle : 0.666 14.191 117118 Z= 0.338 Chirality : 0.038 0.397 14414 Planarity : 0.005 0.070 8812 Dihedral : 23.704 179.598 31546 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.13 % Favored : 89.68 % Rotamer: Outliers : 2.95 % Allowed : 23.72 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 0.90 % Twisted General : 0.28 % 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: -1.86 (0.12), residues: 5153 helix: 0.21 (0.13), residues: 1708 sheet: -1.38 (0.19), residues: 680 loop : -2.21 (0.12), residues: 2765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP t 729 HIS 0.020 0.001 HIS X 18 PHE 0.030 0.002 PHE I 14 TYR 0.043 0.002 TYR R 243 ARG 0.014 0.000 ARG F 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 838 time to evaluate : 4.452 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 TARDY: cannot create tardy model for: "SER t 772 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 25 GLU cc_start: 0.4161 (OUTLIER) cc_final: 0.3847 (pp20) REVERT: D 54 ARG cc_start: 0.7238 (tpp80) cc_final: 0.6851 (ttm110) REVERT: B 46 TRP cc_start: 0.6119 (m-90) cc_final: 0.5684 (m-10) REVERT: B 81 ARG cc_start: 0.7071 (ttt-90) cc_final: 0.6811 (tpt-90) REVERT: B 165 LEU cc_start: 0.7332 (tp) cc_final: 0.6594 (pp) REVERT: C 45 ARG cc_start: 0.3867 (mmm160) cc_final: 0.2872 (mmm-85) REVERT: E 28 MET cc_start: 0.5235 (tmm) cc_final: 0.4815 (tmm) REVERT: E 111 MET cc_start: 0.5327 (mmp) cc_final: 0.5087 (mmm) REVERT: H 56 LYS cc_start: 0.6167 (ttmt) cc_final: 0.5608 (mmtp) REVERT: I 44 GLU cc_start: 0.7368 (tt0) cc_final: 0.7038 (tm-30) REVERT: I 130 ARG cc_start: 0.7063 (tpp80) cc_final: 0.6576 (tmt-80) REVERT: I 134 ARG cc_start: 0.7917 (ptm-80) cc_final: 0.7158 (tpp-160) REVERT: L 27 GLN cc_start: 0.7297 (mt0) cc_final: 0.6872 (mm-40) REVERT: P 7 PHE cc_start: 0.8001 (m-80) cc_final: 0.7784 (m-80) REVERT: P 27 ARG cc_start: 0.7484 (tpp80) cc_final: 0.6897 (tmt170) REVERT: P 38 PHE cc_start: 0.8868 (t80) cc_final: 0.8544 (t80) REVERT: P 43 ASP cc_start: 0.7471 (m-30) cc_final: 0.6915 (t0) REVERT: P 117 GLU cc_start: 0.8990 (tt0) cc_final: 0.8719 (pm20) REVERT: P 123 VAL cc_start: 0.9073 (t) cc_final: 0.8670 (m) REVERT: P 128 SER cc_start: 0.8499 (m) cc_final: 0.8199 (p) REVERT: P 135 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7662 (tp30) REVERT: Q 24 PHE cc_start: 0.7024 (m-10) cc_final: 0.6596 (t80) REVERT: Q 26 ARG cc_start: 0.8151 (ptp-170) cc_final: 0.7831 (ptt-90) REVERT: Q 30 PHE cc_start: 0.8863 (m-80) cc_final: 0.8585 (m-80) REVERT: Q 64 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7611 (ptm160) REVERT: Q 78 ASP cc_start: 0.7244 (p0) cc_final: 0.6932 (p0) REVERT: Q 82 ARG cc_start: 0.8517 (mtp85) cc_final: 0.8008 (mtm180) REVERT: Q 131 ASP cc_start: 0.5768 (p0) cc_final: 0.5353 (p0) REVERT: Q 138 PHE cc_start: 0.9160 (m-80) cc_final: 0.8901 (m-80) REVERT: Q 152 ARG cc_start: 0.8488 (ttt180) cc_final: 0.8119 (ttp-110) REVERT: Q 177 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: R 83 ILE cc_start: 0.8264 (mm) cc_final: 0.8054 (tp) REVERT: R 88 LYS cc_start: 0.6512 (OUTLIER) cc_final: 0.6033 (pttt) REVERT: R 120 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8526 (pt0) REVERT: R 176 SER cc_start: 0.9213 (m) cc_final: 0.8646 (t) REVERT: S 87 MET cc_start: 0.8912 (tpp) cc_final: 0.8427 (tpp) REVERT: S 230 GLU cc_start: 0.7433 (mp0) cc_final: 0.6896 (tm-30) REVERT: T 2 LYS cc_start: 0.7856 (ttmt) cc_final: 0.7560 (mttp) REVERT: T 150 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8140 (pp20) REVERT: T 151 ASP cc_start: 0.7549 (m-30) cc_final: 0.7132 (m-30) REVERT: T 201 GLN cc_start: 0.8849 (mm110) cc_final: 0.8463 (mp10) REVERT: T 203 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8356 (tm-30) REVERT: T 210 GLN cc_start: 0.7823 (mt0) cc_final: 0.7394 (mm110) REVERT: T 218 GLU cc_start: 0.8458 (pp20) cc_final: 0.8016 (mm-30) REVERT: U 16 LEU cc_start: 0.7671 (mt) cc_final: 0.7389 (tt) REVERT: U 28 GLU cc_start: 0.7790 (mt-10) cc_final: 0.6663 (mm-30) REVERT: U 30 SER cc_start: 0.5566 (m) cc_final: 0.5199 (t) REVERT: U 72 LYS cc_start: 0.8146 (mttt) cc_final: 0.7803 (mmmt) REVERT: U 95 GLU cc_start: 0.7207 (tp30) cc_final: 0.6358 (pp20) REVERT: U 158 ASP cc_start: 0.8315 (m-30) cc_final: 0.8046 (m-30) REVERT: U 164 TYR cc_start: 0.7885 (p90) cc_final: 0.7681 (p90) REVERT: U 167 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8453 (mm-30) REVERT: U 184 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8138 (tm-30) REVERT: V 29 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8622 (pt) REVERT: V 46 VAL cc_start: 0.8074 (p) cc_final: 0.7842 (m) REVERT: V 77 ARG cc_start: 0.8330 (ttp-170) cc_final: 0.8123 (mtp-110) REVERT: V 153 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: V 179 CYS cc_start: 0.9276 (t) cc_final: 0.8846 (t) REVERT: W 57 ARG cc_start: 0.8658 (ttp-170) cc_final: 0.8289 (mtp180) REVERT: W 64 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8082 (mm-30) REVERT: W 88 GLU cc_start: 0.9363 (mp0) cc_final: 0.8734 (pp20) REVERT: W 157 ASP cc_start: 0.8268 (t0) cc_final: 0.7700 (m-30) REVERT: W 164 PHE cc_start: 0.7786 (m-80) cc_final: 0.7548 (m-80) REVERT: X 116 ARG cc_start: 0.8888 (mtt90) cc_final: 0.8444 (tpt-90) REVERT: Y 9 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8283 (tptt) REVERT: Y 33 VAL cc_start: 0.8555 (m) cc_final: 0.8223 (p) REVERT: Z 20 TYR cc_start: 0.7173 (t80) cc_final: 0.6901 (t80) REVERT: Z 133 ARG cc_start: 0.8386 (ptm160) cc_final: 0.8157 (ttt-90) REVERT: a 2 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8592 (mm-30) REVERT: a 5 LYS cc_start: 0.7795 (pttt) cc_final: 0.7556 (mmtm) REVERT: a 44 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7357 (mtp85) REVERT: a 49 GLU cc_start: 0.8845 (tp30) cc_final: 0.8449 (tp30) REVERT: b 104 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8553 (pp) REVERT: b 115 GLU cc_start: 0.9085 (tt0) cc_final: 0.8703 (tm-30) REVERT: c 3 LYS cc_start: 0.8441 (mttm) cc_final: 0.8070 (mtpt) REVERT: c 55 GLU cc_start: 0.8026 (pt0) cc_final: 0.7700 (tp30) REVERT: c 59 ILE cc_start: 0.5889 (OUTLIER) cc_final: 0.5519 (pt) REVERT: c 99 ASN cc_start: 0.8004 (m110) cc_final: 0.7494 (t0) REVERT: d 42 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8607 (tm-30) REVERT: d 63 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8573 (tt0) REVERT: d 98 GLU cc_start: 0.9358 (mm-30) cc_final: 0.8671 (pp20) REVERT: f 62 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7056 (mt) REVERT: t 121 LYS cc_start: 0.6464 (mmtt) cc_final: 0.6187 (mttt) REVERT: t 291 ARG cc_start: 0.8250 (mmp80) cc_final: 0.7913 (mmp80) REVERT: t 525 TRP cc_start: 0.8562 (t-100) cc_final: 0.8330 (t-100) REVERT: t 599 GLN cc_start: 0.8384 (tt0) cc_final: 0.8130 (mt0) REVERT: t 623 TYR cc_start: 0.7947 (m-10) cc_final: 0.7687 (m-10) REVERT: t 720 MET cc_start: 0.7004 (mmm) cc_final: 0.6731 (mmm) REVERT: t 735 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7327 (tp) REVERT: t 752 HIS cc_start: 0.6870 (m170) cc_final: 0.5649 (m90) REVERT: t 754 TYR cc_start: 0.7661 (m-10) cc_final: 0.7216 (m-80) REVERT: t 780 MET cc_start: 0.7959 (mmt) cc_final: 0.7500 (tpt) REVERT: g 26 LYS cc_start: 0.6587 (ptmt) cc_final: 0.6374 (mmtm) REVERT: p 196 ASP cc_start: 0.8559 (m-30) cc_final: 0.8326 (t70) REVERT: p 221 ARG cc_start: 0.6609 (mtm-85) cc_final: 0.6256 (mtp-110) REVERT: p 269 ARG cc_start: 0.4423 (ptt180) cc_final: 0.4034 (ttp-170) REVERT: r 65 MET cc_start: 0.2256 (OUTLIER) cc_final: 0.1355 (ttp) REVERT: r 214 MET cc_start: 0.5196 (OUTLIER) cc_final: 0.4566 (ptt) outliers start: 123 outliers final: 96 residues processed: 917 average time/residue: 0.7328 time to fit residues: 1143.0759 Evaluate side-chains 913 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 805 time to evaluate : 4.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 43 ASN Chi-restraints excluded: chain L residue 57 MET Chi-restraints excluded: chain N residue 106 TYR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain P residue 135 GLU Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 177 GLN Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 88 LYS Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 253 ASP Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 166 LEU Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 173 TYR Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 153 GLU Chi-restraints excluded: chain V residue 188 GLU Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 100 LYS Chi-restraints excluded: chain X residue 18 HIS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Y residue 83 GLU Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 81 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain b residue 42 GLN Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 87 GLU Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 121 VAL Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain d residue 14 SER Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain f residue 37 CYS Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 99 ASP Chi-restraints excluded: chain t residue 104 LEU Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 208 VAL Chi-restraints excluded: chain t residue 220 PHE Chi-restraints excluded: chain t residue 277 VAL Chi-restraints excluded: chain t residue 482 PHE Chi-restraints excluded: chain t residue 665 SER Chi-restraints excluded: chain t residue 735 LEU Chi-restraints excluded: chain t residue 737 THR Chi-restraints excluded: chain t residue 751 THR Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 56 MET Chi-restraints excluded: chain p residue 164 LEU Chi-restraints excluded: chain p residue 192 THR Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain p residue 239 HIS Chi-restraints excluded: chain p residue 262 ASN Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain r residue 87 THR Chi-restraints excluded: chain r residue 107 SER Chi-restraints excluded: chain r residue 121 VAL Chi-restraints excluded: chain r residue 182 ASN Chi-restraints excluded: chain r residue 214 MET Chi-restraints excluded: chain r residue 217 ILE Chi-restraints excluded: chain r residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 427 optimal weight: 0.8980 chunk 573 optimal weight: 0.1980 chunk 165 optimal weight: 10.0000 chunk 496 optimal weight: 1.9990 chunk 79 optimal weight: 30.0000 chunk 149 optimal weight: 20.0000 chunk 539 optimal weight: 0.0370 chunk 225 optimal weight: 4.9990 chunk 554 optimal weight: 0.8980 chunk 68 optimal weight: 30.0000 chunk 99 optimal weight: 10.0000 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN I 12 GLN I 43 ASN I 106 GLN ** P 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 GLN Q 208 GLN Q 232 HIS ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 ASN ** b 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 595 ASN p 239 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.170339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.131396 restraints weight = 143315.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130492 restraints weight = 115411.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131765 restraints weight = 84333.311| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 80787 Z= 0.155 Angle : 0.653 13.873 117118 Z= 0.331 Chirality : 0.038 0.379 14414 Planarity : 0.005 0.061 8812 Dihedral : 23.589 179.728 31545 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.38 % Favored : 89.48 % Rotamer: Outliers : 2.76 % Allowed : 24.27 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 0.90 % Twisted General : 0.26 % 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: -1.78 (0.12), residues: 5153 helix: 0.28 (0.13), residues: 1717 sheet: -1.45 (0.19), residues: 702 loop : -2.13 (0.12), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP t 778 HIS 0.036 0.001 HIS X 18 PHE 0.028 0.002 PHE I 14 TYR 0.036 0.001 TYR R 243 ARG 0.008 0.000 ARG E 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19327.88 seconds wall clock time: 334 minutes 27.66 seconds (20067.66 seconds total)