Starting phenix.real_space_refine on Fri Jan 24 07:35:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsl_44869/01_2025/9bsl_44869.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsl_44869/01_2025/9bsl_44869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bsl_44869/01_2025/9bsl_44869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsl_44869/01_2025/9bsl_44869.map" model { file = "/net/cci-nas-00/data/ceres_data/9bsl_44869/01_2025/9bsl_44869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsl_44869/01_2025/9bsl_44869.cif" } resolution = 3.1 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= 0.002 sd= 0.028 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 2423 5.49 5 S 69 5.16 5 C 37849 2.51 5 N 13934 2.21 5 O 21078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 75353 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 51839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2414, 51839 Classifications: {'RNA': 2414} Modifications used: {'rna2p_pur': 253, 'rna2p_pyr': 138, 'rna3p_pur': 1146, 'rna3p_pyr': 877} Link IDs: {'rna2p': 391, 'rna3p': 2022} Chain breaks: 18 Chain: "C" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1895 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1575 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1511 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1285 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 165} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "I" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 753 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "K" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 925 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "N" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "O" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 741 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "S" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "T" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 394 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 50} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "U" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "V" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2119 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 254} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "W" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3239 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 400} Chain breaks: 3 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Y" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1334 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 169} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'GNP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 29.94, per 1000 atoms: 0.40 Number of scatterers: 75353 At special positions: 0 Unit cell: (191.52, 196.65, 227.43, 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 69 16.00 P 2423 15.00 O 21078 8.00 N 13934 7.00 C 37849 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 Atom "ATOM 40712 O5' C A2206 .*. O " rejected from bonding due to valence issues. Atom "ATOM 40153 O4' A A2152 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.30 Conformation dependent library (CDL) restraints added in 3.3 seconds 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5554 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 37 sheets defined 32.1% alpha, 18.9% beta 723 base pairs and 1167 stacking pairs defined. Time for finding SS restraints: 26.16 Creating SS restraints... Processing helix chain 'C' and resid 10 through 14 removed outlier: 3.612A pdb=" N ARG C 14 " --> pdb=" O ASN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 203 removed outlier: 4.509A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 203 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.209A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 62 through 71 removed outlier: 4.336A pdb=" N LYS D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 29 through 43 Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.753A pdb=" N LYS E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 Processing helix chain 'E' and resid 160 through 167 Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'E' and resid 196 through 206 Processing helix chain 'F' and resid 59 through 64 removed outlier: 3.588A pdb=" N ALA F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 82 removed outlier: 3.716A pdb=" N THR F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER F 71 " --> pdb=" O GLY F 67 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY F 74 " --> pdb=" O ARG F 70 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN F 75 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 153 removed outlier: 4.106A pdb=" N ARG F 153 " --> pdb=" O ILE F 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 39 removed outlier: 4.515A pdb=" N GLU G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 63 removed outlier: 3.921A pdb=" N ILE G 63 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 73 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 97 through 108 removed outlier: 3.541A pdb=" N MET G 101 " --> pdb=" O TYR G 97 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU G 102 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 removed outlier: 3.765A pdb=" N LYS G 121 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 109 removed outlier: 4.099A pdb=" N GLU H 108 " --> pdb=" O ARG H 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 104 through 109' Processing helix chain 'H' and resid 111 through 118 Processing helix chain 'I' and resid 78 through 85 Processing helix chain 'I' and resid 136 through 141 Processing helix chain 'J' and resid 9 through 28 removed outlier: 3.521A pdb=" N THR J 22 " --> pdb=" O ARG J 18 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE J 25 " --> pdb=" O THR J 21 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE J 26 " --> pdb=" O THR J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 39 removed outlier: 3.920A pdb=" N GLU J 39 " --> pdb=" O THR J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 54 removed outlier: 3.568A pdb=" N VAL J 44 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU J 45 " --> pdb=" O ARG J 41 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS J 46 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY J 54 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 63 Processing helix chain 'J' and resid 78 through 86 Processing helix chain 'K' and resid 6 through 12 Processing helix chain 'K' and resid 100 through 105 removed outlier: 3.581A pdb=" N LEU K 103 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU K 105 " --> pdb=" O TYR K 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 21 removed outlier: 3.668A pdb=" N LYS L 16 " --> pdb=" O LYS L 12 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL L 17 " --> pdb=" O ARG L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 30 Processing helix chain 'L' and resid 31 through 53 removed outlier: 3.892A pdb=" N ASN L 44 " --> pdb=" O MET L 40 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE L 47 " --> pdb=" O GLY L 43 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG L 51 " --> pdb=" O PHE L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 71 removed outlier: 3.929A pdb=" N LEU L 60 " --> pdb=" O ASP L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 86 Processing helix chain 'L' and resid 94 through 100 removed outlier: 3.858A pdb=" N LEU L 98 " --> pdb=" O LEU L 95 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA L 99 " --> pdb=" O ALA L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 118 removed outlier: 3.981A pdb=" N PHE L 106 " --> pdb=" O ASP L 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 25 removed outlier: 4.129A pdb=" N VAL N 20 " --> pdb=" O LYS N 16 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU N 23 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE N 24 " --> pdb=" O VAL N 20 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG N 25 " --> pdb=" O MET N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 37 Processing helix chain 'N' and resid 42 through 61 removed outlier: 4.605A pdb=" N ILE N 46 " --> pdb=" O ALA N 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 6 Processing helix chain 'O' and resid 14 through 21 Processing helix chain 'O' and resid 35 through 48 Processing helix chain 'R' and resid 2 through 8 Processing helix chain 'R' and resid 9 through 35 removed outlier: 4.339A pdb=" N LYS R 19 " --> pdb=" O GLU R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 65 removed outlier: 3.520A pdb=" N GLU R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU R 61 " --> pdb=" O ILE R 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 27 Processing helix chain 'S' and resid 40 through 50 removed outlier: 3.518A pdb=" N ARG S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 17 Processing helix chain 'T' and resid 18 through 20 No H-bonds generated for 'chain 'T' and resid 18 through 20' Processing helix chain 'U' and resid 8 through 17 Processing helix chain 'U' and resid 17 through 24 removed outlier: 4.132A pdb=" N SER U 24 " --> pdb=" O SER U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 38 Processing helix chain 'V' and resid 7 through 20 removed outlier: 3.711A pdb=" N ALA V 11 " --> pdb=" O PRO V 7 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG V 14 " --> pdb=" O MET V 10 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG V 15 " --> pdb=" O ALA V 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 41 through 48 removed outlier: 3.743A pdb=" N ILE V 47 " --> pdb=" O MET V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 79 Processing helix chain 'V' and resid 92 through 95 Processing helix chain 'V' and resid 96 through 115 removed outlier: 4.954A pdb=" N GLU V 106 " --> pdb=" O GLU V 102 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LYS V 107 " --> pdb=" O ILE V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 142 Processing helix chain 'V' and resid 182 through 193 Processing helix chain 'V' and resid 201 through 217 removed outlier: 3.627A pdb=" N VAL V 205 " --> pdb=" O ASN V 201 " (cutoff:3.500A) Processing helix chain 'V' and resid 217 through 224 Processing helix chain 'V' and resid 234 through 239 removed outlier: 3.729A pdb=" N ASP V 239 " --> pdb=" O ALA V 235 " (cutoff:3.500A) Processing helix chain 'V' and resid 258 through 269 removed outlier: 4.071A pdb=" N VAL V 262 " --> pdb=" O LYS V 258 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE V 267 " --> pdb=" O ILE V 263 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG V 268 " --> pdb=" O ILE V 264 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR V 269 " --> pdb=" O ARG V 265 " (cutoff:3.500A) Processing helix chain 'W' and resid 15 through 24 removed outlier: 3.691A pdb=" N ALA W 24 " --> pdb=" O PHE W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 83 removed outlier: 3.893A pdb=" N GLU W 82 " --> pdb=" O ILE W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 109 removed outlier: 3.941A pdb=" N ILE W 106 " --> pdb=" O GLU W 102 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU W 107 " --> pdb=" O VAL W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 124 through 130 removed outlier: 3.629A pdb=" N ILE W 130 " --> pdb=" O ARG W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 137 removed outlier: 3.644A pdb=" N SER W 135 " --> pdb=" O ASP W 132 " (cutoff:3.500A) Processing helix chain 'W' and resid 151 through 161 Processing helix chain 'W' and resid 187 through 194 Processing helix chain 'W' and resid 245 through 258 removed outlier: 4.259A pdb=" N LEU W 249 " --> pdb=" O LYS W 245 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG W 250 " --> pdb=" O TYR W 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE W 255 " --> pdb=" O ALA W 251 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP W 256 " --> pdb=" O LEU W 252 " (cutoff:3.500A) Processing helix chain 'W' and resid 272 through 285 removed outlier: 3.920A pdb=" N LYS W 276 " --> pdb=" O ILE W 272 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG W 277 " --> pdb=" O GLU W 273 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR W 281 " --> pdb=" O ARG W 277 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA W 282 " --> pdb=" O ILE W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 304 through 317 removed outlier: 4.123A pdb=" N PHE W 309 " --> pdb=" O THR W 305 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG W 314 " --> pdb=" O GLU W 310 " (cutoff:3.500A) Processing helix chain 'W' and resid 335 through 337 No H-bonds generated for 'chain 'W' and resid 335 through 337' Processing helix chain 'W' and resid 338 through 351 removed outlier: 3.763A pdb=" N ALA W 342 " --> pdb=" O THR W 338 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS W 345 " --> pdb=" O PRO W 341 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU W 348 " --> pdb=" O ILE W 344 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN W 349 " --> pdb=" O LYS W 345 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER W 351 " --> pdb=" O SER W 347 " (cutoff:3.500A) Processing helix chain 'W' and resid 355 through 370 removed outlier: 3.511A pdb=" N ILE W 363 " --> pdb=" O LEU W 359 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET W 364 " --> pdb=" O ASN W 360 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP W 365 " --> pdb=" O ASP W 361 " (cutoff:3.500A) Processing helix chain 'W' and resid 401 through 405 Processing helix chain 'W' and resid 406 through 421 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 4.395A pdb=" N ALA Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 58 removed outlier: 4.400A pdb=" N ASP Y 56 " --> pdb=" O ARG Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 80 through 85 removed outlier: 3.676A pdb=" N LYS Y 83 " --> pdb=" O LYS Y 80 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA Y 84 " --> pdb=" O GLY Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 105 Processing helix chain 'Y' and resid 120 through 128 Processing helix chain 'Y' and resid 148 through 157 removed outlier: 3.519A pdb=" N GLY Y 154 " --> pdb=" O GLU Y 150 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU Y 155 " --> pdb=" O LYS Y 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE Y 156 " --> pdb=" O ALA Y 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 183 through 199 removed outlier: 4.107A pdb=" N GLU Y 187 " --> pdb=" O GLU Y 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.605A pdb=" N ILE C 91 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG C 77 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.543A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL C 181 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 16 removed outlier: 6.735A pdb=" N VAL D 27 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR D 170 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY D 112 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLN D 172 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL D 110 " --> pdb=" O GLN D 172 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 84 removed outlier: 4.223A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLY D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL D 35 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 116 through 120 removed outlier: 5.797A pdb=" N MET D 164 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE D 119 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY D 162 " --> pdb=" O PHE D 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 13 through 18 removed outlier: 4.767A pdb=" N GLY E 15 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N ILE E 123 " --> pdb=" O LYS E 3 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA E 5 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL E 125 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N THR E 195 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL E 155 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 156 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 16 through 19 Processing sheet with id=AB1, first strand: chain 'F' and resid 122 through 124 Processing sheet with id=AB2, first strand: chain 'F' and resid 104 through 107 Processing sheet with id=AB3, first strand: chain 'G' and resid 123 through 125 removed outlier: 6.289A pdb=" N VAL G 55 " --> pdb=" O ASN G 124 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TRP G 16 " --> pdb=" O GLU G 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 74 through 78 Processing sheet with id=AB5, first strand: chain 'H' and resid 7 through 10 removed outlier: 3.682A pdb=" N VAL H 19 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL H 10 " --> pdb=" O ARG H 17 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG H 17 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN H 45 " --> pdb=" O ARG H 17 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL H 19 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL H 43 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR H 21 " --> pdb=" O CYS H 41 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N CYS H 41 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS H 23 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ILE H 39 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS H 59 " --> pdb=" O ILE H 87 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA H 83 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N CYS H 84 " --> pdb=" O ARG H 7 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LYS H 9 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE H 86 " --> pdb=" O LYS H 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 76 through 78 removed outlier: 7.446A pdb=" N SER K 59 " --> pdb=" O GLY K 55 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLY K 55 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR K 61 " --> pdb=" O ARG K 53 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG K 53 " --> pdb=" O THR K 61 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR K 63 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE K 67 " --> pdb=" O GLU K 47 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N GLU K 47 " --> pdb=" O ILE K 67 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N THR K 28 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL K 89 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG K 30 " --> pdb=" O ILE K 87 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE K 87 " --> pdb=" O ARG K 30 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N HIS K 32 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 102 through 103 removed outlier: 6.186A pdb=" N VAL H 102 " --> pdb=" O ILE H 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'I' and resid 75 through 77 removed outlier: 5.923A pdb=" N ALA I 75 " --> pdb=" O LYS I 110 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS I 127 " --> pdb=" O VAL I 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 29 through 33 removed outlier: 4.665A pdb=" N GLY J 105 " --> pdb=" O MET J 114 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE J 116 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS J 103 " --> pdb=" O ILE J 116 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLU J 118 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE J 101 " --> pdb=" O GLU J 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 10 through 14 removed outlier: 6.514A pdb=" N ILE M 4 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 19 through 22 removed outlier: 4.000A pdb=" N LYS M 64 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR M 96 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL M 62 " --> pdb=" O THR M 96 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU M 98 " --> pdb=" O ALA M 60 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA M 60 " --> pdb=" O GLU M 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 71 through 77 removed outlier: 4.012A pdb=" N VAL M 82 " --> pdb=" O LYS M 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 3 through 10 removed outlier: 5.888A pdb=" N SER N 101 " --> pdb=" O THR N 9 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER N 108 " --> pdb=" O ILE N 71 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE N 71 " --> pdb=" O SER N 108 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 82 through 88 removed outlier: 3.771A pdb=" N ARG N 92 " --> pdb=" O ARG N 88 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 8 through 11 removed outlier: 3.614A pdb=" N ARG O 10 " --> pdb=" O GLU O 29 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG O 77 " --> pdb=" O VAL O 30 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS O 53 " --> pdb=" O LYS O 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 63 through 66 Processing sheet with id=AC8, first strand: chain 'P' and resid 63 through 64 removed outlier: 3.655A pdb=" N ALA P 25 " --> pdb=" O LEU P 34 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 41 through 45 Processing sheet with id=AD1, first strand: chain 'P' and resid 81 through 86 removed outlier: 4.365A pdb=" N LYS P 84 " --> pdb=" O VAL P 91 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL P 91 " --> pdb=" O LYS P 84 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 34 through 38 Processing sheet with id=AD3, first strand: chain 'T' and resid 48 through 49 Processing sheet with id=AD4, first strand: chain 'V' and resid 81 through 84 removed outlier: 4.688A pdb=" N ARG V 81 " --> pdb=" O ARG V 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN V 159 " --> pdb=" O ASP V 171 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 42 through 46 removed outlier: 6.362A pdb=" N VAL W 6 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL W 5 " --> pdb=" O VAL W 85 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE W 87 " --> pdb=" O VAL W 5 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ALA W 7 " --> pdb=" O ILE W 87 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET W 89 " --> pdb=" O ALA W 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL W 9 " --> pdb=" O MET W 89 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL W 115 " --> pdb=" O ILE W 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'W' and resid 176 through 178 removed outlier: 4.160A pdb=" N ILE W 176 " --> pdb=" O GLU W 224 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL W 228 " --> pdb=" O PHE W 178 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL W 214 " --> pdb=" O ASP W 229 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'W' and resid 181 through 182 removed outlier: 6.672A pdb=" N VAL W 261 " --> pdb=" O VAL W 290 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL W 292 " --> pdb=" O VAL W 261 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL W 263 " --> pdb=" O VAL W 292 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASN W 294 " --> pdb=" O VAL W 263 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU W 265 " --> pdb=" O ASN W 294 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 382 through 387 removed outlier: 3.691A pdb=" N TYR W 384 " --> pdb=" O PHE W 398 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N PHE W 395 " --> pdb=" O PHE W 431 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ARG W 433 " --> pdb=" O PHE W 395 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL W 397 " --> pdb=" O ARG W 433 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 170 through 177 removed outlier: 4.216A pdb=" N ILE Y 171 " --> pdb=" O PHE Y 46 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE Y 46 " --> pdb=" O ILE Y 171 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL Y 173 " --> pdb=" O VAL Y 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE Y 175 " --> pdb=" O VAL Y 42 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL Y 42 " --> pdb=" O ILE Y 175 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN Y 211 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 75 through 76 803 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1848 hydrogen bonds 3020 hydrogen bond angles 0 basepair planarities 723 basepair parallelities 1167 stacking parallelities Total time for adding SS restraints: 88.71 Time building geometry restraints manager: 16.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11533 1.33 - 1.45: 33969 1.45 - 1.57: 31412 1.57 - 1.69: 4820 1.69 - 1.81: 135 Bond restraints: 81869 Sorted by residual: bond pdb=" CA ARG Y 129 " pdb=" C ARG Y 129 " ideal model delta sigma weight residual 1.523 1.611 -0.089 1.61e-02 3.86e+03 3.03e+01 bond pdb=" N3B GNP V 301 " pdb=" PG GNP V 301 " ideal model delta sigma weight residual 1.801 1.700 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N3B GNP W 501 " pdb=" PG GNP W 501 " ideal model delta sigma weight residual 1.801 1.704 0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" N3B GNP W 502 " pdb=" PG GNP W 502 " ideal model delta sigma weight residual 1.801 1.706 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O5' GNP V 301 " pdb=" PA GNP V 301 " ideal model delta sigma weight residual 1.660 1.568 0.092 2.00e-02 2.50e+03 2.12e+01 ... (remaining 81864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 121773 3.24 - 6.48: 699 6.48 - 9.72: 57 9.72 - 12.97: 10 12.97 - 16.21: 3 Bond angle restraints: 122542 Sorted by residual: angle pdb=" N ILE W 23 " pdb=" CA ILE W 23 " pdb=" C ILE W 23 " ideal model delta sigma weight residual 110.42 101.16 9.26 9.60e-01 1.09e+00 9.30e+01 angle pdb=" N LYS Y 54 " pdb=" CA LYS Y 54 " pdb=" CB LYS Y 54 " ideal model delta sigma weight residual 110.56 98.42 12.14 1.38e+00 5.25e-01 7.74e+01 angle pdb=" N LYS Y 198 " pdb=" CA LYS Y 198 " pdb=" C LYS Y 198 " ideal model delta sigma weight residual 111.33 100.91 10.42 1.21e+00 6.83e-01 7.42e+01 angle pdb=" N LYS Y 54 " pdb=" CA LYS Y 54 " pdb=" C LYS Y 54 " ideal model delta sigma weight residual 112.93 122.41 -9.48 1.12e+00 7.97e-01 7.17e+01 angle pdb=" N GLY Y 61 " pdb=" CA GLY Y 61 " pdb=" C GLY Y 61 " ideal model delta sigma weight residual 110.55 123.78 -13.23 1.64e+00 3.72e-01 6.51e+01 ... (remaining 122537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 45415 35.93 - 71.85: 6103 71.85 - 107.78: 749 107.78 - 143.71: 36 143.71 - 179.63: 35 Dihedral angle restraints: 52338 sinusoidal: 43721 harmonic: 8617 Sorted by residual: dihedral pdb=" O4' C A1515 " pdb=" C1' C A1515 " pdb=" N1 C A1515 " pdb=" C2 C A1515 " ideal model delta sinusoidal sigma weight residual -160.00 19.63 -179.63 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 482 " pdb=" C1' C A 482 " pdb=" N1 C A 482 " pdb=" C2 C A 482 " ideal model delta sinusoidal sigma weight residual -160.00 18.00 -178.00 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1281 " pdb=" C1' C A1281 " pdb=" N1 C A1281 " pdb=" C2 C A1281 " ideal model delta sinusoidal sigma weight residual -160.00 17.46 -177.46 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 52335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 14301 0.063 - 0.126: 1236 0.126 - 0.188: 151 0.188 - 0.251: 27 0.251 - 0.314: 6 Chirality restraints: 15721 Sorted by residual: chirality pdb=" CA PRO Y 52 " pdb=" N PRO Y 52 " pdb=" C PRO Y 52 " pdb=" CB PRO Y 52 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ASN W 21 " pdb=" N ASN W 21 " pdb=" C ASN W 21 " pdb=" CB ASN W 21 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ARG Y 129 " pdb=" N ARG Y 129 " pdb=" C ARG Y 129 " pdb=" CB ARG Y 129 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 15718 not shown) Planarity restraints: 6529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP Y 119 " -0.022 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C ASP Y 119 " 0.079 2.00e-02 2.50e+03 pdb=" O ASP Y 119 " -0.030 2.00e-02 2.50e+03 pdb=" N MET Y 120 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 471 " 0.006 2.00e-02 2.50e+03 1.84e-02 1.01e+01 pdb=" N9 G A 471 " 0.002 2.00e-02 2.50e+03 pdb=" C8 G A 471 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G A 471 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 471 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 471 " -0.016 2.00e-02 2.50e+03 pdb=" O6 G A 471 " 0.018 2.00e-02 2.50e+03 pdb=" N1 G A 471 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G A 471 " -0.049 2.00e-02 2.50e+03 pdb=" N2 G A 471 " 0.031 2.00e-02 2.50e+03 pdb=" N3 G A 471 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G A 471 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR H 47 " 0.051 5.00e-02 4.00e+02 7.79e-02 9.72e+00 pdb=" N PRO H 48 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO H 48 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 48 " 0.043 5.00e-02 4.00e+02 ... (remaining 6526 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 8 1.80 - 2.58: 701 2.58 - 3.35: 86143 3.35 - 4.13: 228087 4.13 - 4.90: 336417 Nonbonded interactions: 651356 Sorted by model distance: nonbonded pdb=" OH TYR W 131 " pdb=" CA GLY Y 122 " model vdw 1.028 3.440 nonbonded pdb=" O5' C A2206 " pdb=" CB ALA Y 213 " model vdw 1.340 3.460 nonbonded pdb=" O4' A A2152 " pdb=" CE1 HIS Y 172 " model vdw 1.436 3.260 nonbonded pdb=" OP1 A A2152 " pdb=" NE2 HIS Y 172 " model vdw 1.611 3.120 nonbonded pdb=" OP1 C A2206 " pdb=" CA ALA Y 213 " model vdw 1.661 3.470 ... (remaining 651351 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 2.460 Check model and map are aligned: 0.420 Set scattering table: 0.530 Process input model: 195.990 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 209.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 81869 Z= 0.210 Angle : 0.673 16.207 122542 Z= 0.356 Chirality : 0.038 0.314 15721 Planarity : 0.004 0.078 6529 Dihedral : 24.740 179.632 46784 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.17 % Rotamer: Outliers : 0.73 % Allowed : 20.24 % Favored : 79.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 2962 helix: 0.17 (0.19), residues: 871 sheet: -0.39 (0.22), residues: 532 loop : -1.53 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP W 296 HIS 0.008 0.001 HIS F 39 PHE 0.029 0.001 PHE Y 78 TYR 0.021 0.001 TYR Y 193 ARG 0.010 0.000 ARG R 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 692 time to evaluate : 3.441 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 33 ASN cc_start: 0.7862 (m-40) cc_final: 0.7644 (m-40) REVERT: D 95 GLN cc_start: 0.6116 (tt0) cc_final: 0.5912 (tt0) REVERT: F 34 LEU cc_start: 0.4418 (mt) cc_final: 0.4022 (tp) REVERT: F 55 ARG cc_start: 0.6714 (ptt180) cc_final: 0.6283 (ptp90) REVERT: F 86 ARG cc_start: 0.3308 (mmm-85) cc_final: 0.0728 (ttt-90) REVERT: H 37 ASP cc_start: 0.8137 (m-30) cc_final: 0.7838 (m-30) REVERT: H 112 MET cc_start: 0.8479 (mmm) cc_final: 0.7955 (mmm) REVERT: L 85 LEU cc_start: 0.8230 (tt) cc_final: 0.8020 (mt) REVERT: N 22 ASP cc_start: 0.8970 (m-30) cc_final: 0.8644 (m-30) REVERT: O 31 ASP cc_start: 0.8626 (t0) cc_final: 0.8366 (t0) REVERT: P 39 ASN cc_start: 0.8657 (t0) cc_final: 0.8183 (t0) REVERT: S 17 GLU cc_start: 0.7431 (tp30) cc_final: 0.7208 (tp30) REVERT: T 29 GLU cc_start: 0.7842 (tm-30) cc_final: 0.6806 (mp0) REVERT: V 95 GLN cc_start: 0.8735 (pt0) cc_final: 0.8482 (pp30) REVERT: V 216 HIS cc_start: 0.8191 (m-70) cc_final: 0.7815 (m-70) REVERT: W 162 HIS cc_start: 0.7793 (m-70) cc_final: 0.7532 (m-70) REVERT: W 233 MET cc_start: 0.8213 (mtp) cc_final: 0.7815 (mtt) REVERT: W 281 TYR cc_start: 0.8531 (m-80) cc_final: 0.8320 (m-80) REVERT: W 283 HIS cc_start: 0.8508 (t70) cc_final: 0.8127 (t-90) REVERT: Y 57 GLN cc_start: 0.4086 (OUTLIER) cc_final: 0.3554 (pm20) REVERT: Y 205 LYS cc_start: 0.5305 (OUTLIER) cc_final: 0.4293 (mmtt) outliers start: 18 outliers final: 2 residues processed: 702 average time/residue: 0.7572 time to fit residues: 891.3398 Evaluate side-chains 409 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 405 time to evaluate : 3.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 133 LYS Chi-restraints excluded: chain Y residue 57 GLN Chi-restraints excluded: chain Y residue 130 VAL Chi-restraints excluded: chain Y residue 205 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 450 optimal weight: 0.9980 chunk 403 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 272 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 417 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 254 optimal weight: 8.9990 chunk 310 optimal weight: 8.9990 chunk 484 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 GLN S 52 HIS V 203 GLN V 216 HIS W 294 ASN W 312 ASN Y 57 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.074843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.049259 restraints weight = 304882.425| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.71 r_work: 0.2810 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 81869 Z= 0.288 Angle : 0.716 10.096 122542 Z= 0.363 Chirality : 0.040 0.331 15721 Planarity : 0.005 0.096 6529 Dihedral : 25.030 179.885 40938 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.27 % Rotamer: Outliers : 4.53 % Allowed : 19.56 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 2962 helix: -0.04 (0.17), residues: 908 sheet: -0.52 (0.21), residues: 575 loop : -1.43 (0.15), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP W 296 HIS 0.040 0.002 HIS Y 172 PHE 0.037 0.003 PHE W 88 TYR 0.017 0.002 TYR W 43 ARG 0.015 0.001 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 418 time to evaluate : 3.380 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: C 27 ASP cc_start: 0.8730 (p0) cc_final: 0.8517 (p0) REVERT: D 21 ASP cc_start: 0.8646 (m-30) cc_final: 0.8113 (m-30) REVERT: D 95 GLN cc_start: 0.7659 (tt0) cc_final: 0.7370 (tt0) REVERT: F 50 VAL cc_start: 0.5541 (OUTLIER) cc_final: 0.5203 (t) REVERT: F 55 ARG cc_start: 0.7003 (ptt180) cc_final: 0.6740 (ptp90) REVERT: F 71 SER cc_start: 0.6603 (t) cc_final: 0.6256 (p) REVERT: F 75 ASN cc_start: 0.5738 (t0) cc_final: 0.5279 (t0) REVERT: F 78 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6620 (pt0) REVERT: G 8 ASN cc_start: 0.8719 (t0) cc_final: 0.8341 (m110) REVERT: G 118 GLN cc_start: 0.9368 (tm-30) cc_final: 0.8936 (tm-30) REVERT: H 44 LYS cc_start: 0.9096 (ttmm) cc_final: 0.8687 (ttpp) REVERT: I 71 ARG cc_start: 0.4683 (mtp180) cc_final: 0.3577 (mtp85) REVERT: I 74 TYR cc_start: 0.6730 (m-80) cc_final: 0.6528 (m-80) REVERT: I 79 LEU cc_start: 0.7895 (tp) cc_final: 0.7579 (tp) REVERT: J 85 SER cc_start: 0.9147 (t) cc_final: 0.8732 (p) REVERT: J 102 MET cc_start: 0.8155 (mtp) cc_final: 0.7755 (mtm) REVERT: L 80 MET cc_start: 0.9510 (OUTLIER) cc_final: 0.9306 (mmt) REVERT: O 3 ASP cc_start: 0.8199 (t0) cc_final: 0.7821 (t0) REVERT: O 65 ARG cc_start: 0.8117 (ptm-80) cc_final: 0.7879 (ptm-80) REVERT: O 69 TYR cc_start: 0.8361 (m-80) cc_final: 0.8108 (m-80) REVERT: O 72 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8643 (mmm) REVERT: P 39 ASN cc_start: 0.8878 (t0) cc_final: 0.8530 (t0) REVERT: R 8 ASP cc_start: 0.8579 (t0) cc_final: 0.8339 (t0) REVERT: R 17 LYS cc_start: 0.8823 (mmmm) cc_final: 0.8623 (mmmm) REVERT: R 31 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8798 (mp10) REVERT: S 44 ARG cc_start: 0.8626 (mmt-90) cc_final: 0.8325 (mpt180) REVERT: T 29 GLU cc_start: 0.8053 (tm-30) cc_final: 0.6830 (mp0) REVERT: V 78 GLN cc_start: 0.7945 (mt0) cc_final: 0.7598 (mp10) REVERT: V 102 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8820 (pp20) REVERT: V 112 ARG cc_start: 0.9298 (ptp-110) cc_final: 0.9041 (ptp90) REVERT: V 133 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8283 (mtmm) REVERT: W 148 HIS cc_start: 0.3151 (m90) cc_final: 0.2236 (m-70) REVERT: W 162 HIS cc_start: 0.7807 (m-70) cc_final: 0.7267 (m90) REVERT: W 176 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8123 (pp) REVERT: W 223 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8731 (tp40) REVERT: W 269 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: W 281 TYR cc_start: 0.8975 (m-80) cc_final: 0.8381 (m-80) REVERT: W 309 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7560 (t80) REVERT: W 318 GLN cc_start: 0.8937 (mt0) cc_final: 0.8535 (tt0) REVERT: Y 56 ASP cc_start: 0.5081 (OUTLIER) cc_final: 0.4318 (p0) REVERT: Y 109 PHE cc_start: 0.6858 (t80) cc_final: 0.6363 (m-80) REVERT: Y 192 MET cc_start: -0.1137 (ppp) cc_final: -0.1694 (ppp) outliers start: 112 outliers final: 44 residues processed: 503 average time/residue: 0.7141 time to fit residues: 617.9019 Evaluate side-chains 403 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 350 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 31 GLN Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain V residue 133 LYS Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 263 ILE Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain W residue 269 GLU Chi-restraints excluded: chain W residue 309 PHE Chi-restraints excluded: chain W residue 331 LEU Chi-restraints excluded: chain W residue 344 ILE Chi-restraints excluded: chain W residue 359 LEU Chi-restraints excluded: chain W residue 426 THR Chi-restraints excluded: chain Y residue 56 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 247 optimal weight: 8.9990 chunk 354 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 242 optimal weight: 0.0870 chunk 61 optimal weight: 10.0000 chunk 359 optimal weight: 5.9990 chunk 480 optimal weight: 8.9990 chunk 364 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 GLN E 121 ASN G 48 HIS I 106 ASN K 32 HIS S 52 HIS T 50 ASN ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.073234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.047557 restraints weight = 303220.685| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.76 r_work: 0.2753 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 81869 Z= 0.291 Angle : 0.675 13.441 122542 Z= 0.342 Chirality : 0.039 0.312 15721 Planarity : 0.005 0.098 6529 Dihedral : 24.938 179.052 40930 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.40 % Allowed : 19.84 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 2962 helix: 0.36 (0.18), residues: 894 sheet: -0.35 (0.21), residues: 600 loop : -1.48 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP W 296 HIS 0.013 0.001 HIS S 52 PHE 0.027 0.002 PHE Y 189 TYR 0.015 0.002 TYR F 110 ARG 0.013 0.001 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 375 time to evaluate : 3.478 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: D 95 GLN cc_start: 0.8663 (tt0) cc_final: 0.8453 (tt0) REVERT: D 167 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8331 (pm20) REVERT: D 204 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8776 (p) REVERT: E 65 TRP cc_start: 0.6187 (p-90) cc_final: 0.5186 (p-90) REVERT: F 71 SER cc_start: 0.6908 (t) cc_final: 0.6515 (p) REVERT: F 75 ASN cc_start: 0.5703 (t0) cc_final: 0.5125 (t0) REVERT: F 78 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6577 (pt0) REVERT: G 118 GLN cc_start: 0.9254 (tm-30) cc_final: 0.8788 (tm-30) REVERT: H 81 GLU cc_start: 0.9233 (pm20) cc_final: 0.8708 (pm20) REVERT: J 19 ASP cc_start: 0.9107 (m-30) cc_final: 0.8714 (m-30) REVERT: J 85 SER cc_start: 0.9107 (t) cc_final: 0.8745 (m) REVERT: J 102 MET cc_start: 0.8177 (mtp) cc_final: 0.7851 (mtm) REVERT: L 49 ASP cc_start: 0.9316 (m-30) cc_final: 0.9001 (m-30) REVERT: M 24 LYS cc_start: 0.9527 (OUTLIER) cc_final: 0.9291 (ttpp) REVERT: N 22 ASP cc_start: 0.9290 (m-30) cc_final: 0.8913 (m-30) REVERT: O 3 ASP cc_start: 0.8271 (t0) cc_final: 0.7745 (t0) REVERT: O 6 ASP cc_start: 0.8934 (m-30) cc_final: 0.8717 (m-30) REVERT: O 31 ASP cc_start: 0.8661 (t0) cc_final: 0.8424 (t0) REVERT: O 41 ASP cc_start: 0.9127 (t0) cc_final: 0.8904 (m-30) REVERT: O 65 ARG cc_start: 0.8053 (ptm-80) cc_final: 0.7558 (ptm-80) REVERT: O 89 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8412 (tp30) REVERT: P 31 ASP cc_start: 0.8844 (t0) cc_final: 0.8577 (t0) REVERT: P 36 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8711 (tm-30) REVERT: P 39 ASN cc_start: 0.8890 (t0) cc_final: 0.8601 (t0) REVERT: R 29 ARG cc_start: 0.8959 (mtm-85) cc_final: 0.8567 (mtt-85) REVERT: R 31 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8436 (mp10) REVERT: S 9 LYS cc_start: 0.8484 (tttm) cc_final: 0.8277 (ptmm) REVERT: S 10 ARG cc_start: 0.8584 (mtp85) cc_final: 0.8097 (mtt90) REVERT: S 44 ARG cc_start: 0.8611 (mmt-90) cc_final: 0.8385 (mmt-90) REVERT: S 51 SER cc_start: 0.8833 (p) cc_final: 0.8391 (m) REVERT: T 29 GLU cc_start: 0.8049 (tm-30) cc_final: 0.6850 (mp0) REVERT: V 22 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8996 (mmmt) REVERT: V 70 GLN cc_start: 0.9408 (tt0) cc_final: 0.8971 (tm-30) REVERT: V 95 GLN cc_start: 0.8632 (pp30) cc_final: 0.8390 (pp30) REVERT: V 102 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8806 (pp20) REVERT: V 112 ARG cc_start: 0.9314 (ptp-110) cc_final: 0.9021 (ptp90) REVERT: V 157 SER cc_start: 0.9050 (m) cc_final: 0.8808 (t) REVERT: V 165 LYS cc_start: 0.8571 (tptp) cc_final: 0.8279 (pptt) REVERT: V 184 LEU cc_start: 0.8837 (tp) cc_final: 0.8623 (pt) REVERT: W 148 HIS cc_start: 0.3241 (m90) cc_final: 0.2899 (m90) REVERT: W 162 HIS cc_start: 0.7836 (m-70) cc_final: 0.7483 (m-70) REVERT: W 269 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: W 278 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.9046 (tp) REVERT: W 281 TYR cc_start: 0.8970 (m-80) cc_final: 0.8402 (m-80) REVERT: W 309 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7684 (t80) REVERT: W 318 GLN cc_start: 0.9107 (mt0) cc_final: 0.8665 (tt0) REVERT: W 326 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8908 (mm) REVERT: W 340 MET cc_start: 0.8965 (mmm) cc_final: 0.8618 (tmm) REVERT: Y 56 ASP cc_start: 0.4912 (OUTLIER) cc_final: 0.4414 (p0) outliers start: 109 outliers final: 63 residues processed: 453 average time/residue: 0.7288 time to fit residues: 567.3408 Evaluate side-chains 409 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 336 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 31 GLN Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 22 LYS Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 210 LEU Chi-restraints excluded: chain V residue 234 ILE Chi-restraints excluded: chain V residue 263 ILE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain W residue 269 GLU Chi-restraints excluded: chain W residue 278 ILE Chi-restraints excluded: chain W residue 309 PHE Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 405 MET Chi-restraints excluded: chain W residue 426 THR Chi-restraints excluded: chain Y residue 56 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 178 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 400 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 522 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 474 optimal weight: 6.9990 chunk 243 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 HIS G 8 ASN R 31 GLN ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 HIS V 203 GLN ** Y 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.071628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.046128 restraints weight = 303100.543| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.70 r_work: 0.2716 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 81869 Z= 0.375 Angle : 0.731 11.965 122542 Z= 0.369 Chirality : 0.041 0.322 15721 Planarity : 0.005 0.085 6529 Dihedral : 24.929 178.857 40926 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.21 % Allowed : 20.61 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.15), residues: 2962 helix: 0.42 (0.18), residues: 885 sheet: -0.37 (0.21), residues: 582 loop : -1.55 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP W 296 HIS 0.009 0.001 HIS S 52 PHE 0.015 0.002 PHE K 77 TYR 0.017 0.002 TYR C 83 ARG 0.006 0.001 ARG R 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 347 time to evaluate : 3.338 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: C 272 ARG cc_start: 0.8438 (tmm-80) cc_final: 0.8148 (tmm-80) REVERT: D 21 ASP cc_start: 0.8531 (m-30) cc_final: 0.7973 (m-30) REVERT: D 167 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: E 16 ASP cc_start: 0.8804 (m-30) cc_final: 0.8517 (p0) REVERT: F 71 SER cc_start: 0.6985 (t) cc_final: 0.6370 (m) REVERT: F 78 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6660 (pt0) REVERT: G 72 ASP cc_start: 0.8455 (m-30) cc_final: 0.8187 (m-30) REVERT: G 118 GLN cc_start: 0.9388 (tm-30) cc_final: 0.8886 (tm-30) REVERT: H 44 LYS cc_start: 0.9357 (ttmm) cc_final: 0.9140 (ttmm) REVERT: H 112 MET cc_start: 0.8842 (mmm) cc_final: 0.8460 (mmm) REVERT: I 117 LEU cc_start: 0.6075 (mt) cc_final: 0.5772 (mt) REVERT: J 85 SER cc_start: 0.9176 (t) cc_final: 0.8735 (p) REVERT: J 86 ASP cc_start: 0.8983 (p0) cc_final: 0.8741 (p0) REVERT: K 105 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8358 (mp0) REVERT: L 49 ASP cc_start: 0.9228 (m-30) cc_final: 0.8938 (m-30) REVERT: L 56 ASP cc_start: 0.9330 (OUTLIER) cc_final: 0.9051 (m-30) REVERT: N 22 ASP cc_start: 0.9249 (m-30) cc_final: 0.8926 (m-30) REVERT: O 3 ASP cc_start: 0.8412 (t0) cc_final: 0.7960 (t0) REVERT: O 23 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8932 (mp0) REVERT: O 41 ASP cc_start: 0.9047 (t0) cc_final: 0.8840 (t0) REVERT: O 72 MET cc_start: 0.9298 (mtp) cc_final: 0.8900 (mmm) REVERT: O 89 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8395 (tp30) REVERT: P 31 ASP cc_start: 0.8820 (t0) cc_final: 0.8556 (t0) REVERT: P 39 ASN cc_start: 0.9032 (t0) cc_final: 0.8792 (t0) REVERT: P 40 MET cc_start: 0.9277 (mmt) cc_final: 0.8855 (mmm) REVERT: R 8 ASP cc_start: 0.8446 (t0) cc_final: 0.8198 (t0) REVERT: R 9 LEU cc_start: 0.8122 (tp) cc_final: 0.7806 (tt) REVERT: R 29 ARG cc_start: 0.8895 (mtm-85) cc_final: 0.8605 (mtt-85) REVERT: R 30 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8374 (t80) REVERT: S 51 SER cc_start: 0.8939 (p) cc_final: 0.8358 (m) REVERT: T 29 GLU cc_start: 0.8051 (tm-30) cc_final: 0.6571 (mp0) REVERT: V 108 PHE cc_start: 0.8626 (m-10) cc_final: 0.8304 (m-10) REVERT: V 112 ARG cc_start: 0.9259 (ptp-110) cc_final: 0.9037 (ptp90) REVERT: V 165 LYS cc_start: 0.8775 (tptp) cc_final: 0.8498 (pptt) REVERT: V 184 LEU cc_start: 0.8943 (tp) cc_final: 0.8687 (pt) REVERT: W 162 HIS cc_start: 0.7919 (m-70) cc_final: 0.7470 (m-70) REVERT: W 269 GLU cc_start: 0.8119 (mp0) cc_final: 0.7867 (pm20) REVERT: W 281 TYR cc_start: 0.8881 (m-80) cc_final: 0.8373 (m-80) REVERT: W 318 GLN cc_start: 0.9244 (mt0) cc_final: 0.8924 (mm-40) REVERT: W 326 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8926 (mm) REVERT: W 365 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8945 (t0) REVERT: Y 56 ASP cc_start: 0.4924 (OUTLIER) cc_final: 0.4454 (p0) REVERT: Y 126 LYS cc_start: 0.4388 (mmtt) cc_final: 0.3572 (tptp) outliers start: 129 outliers final: 89 residues processed: 442 average time/residue: 0.6946 time to fit residues: 535.1192 Evaluate side-chains 419 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 323 time to evaluate : 4.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 78 GLU Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 210 LEU Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 263 ILE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 331 LEU Chi-restraints excluded: chain W residue 365 ASP Chi-restraints excluded: chain W residue 405 MET Chi-restraints excluded: chain W residue 426 THR Chi-restraints excluded: chain Y residue 56 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 198 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 376 optimal weight: 2.9990 chunk 417 optimal weight: 3.9990 chunk 429 optimal weight: 9.9990 chunk 470 optimal weight: 2.9990 chunk 363 optimal weight: 8.9990 chunk 463 optimal weight: 0.5980 chunk 400 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 188 optimal weight: 50.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 GLN S 52 HIS V 158 GLN V 203 GLN ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.073099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.047937 restraints weight = 301518.335| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.72 r_work: 0.2767 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 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 0.051 81869 Z= 0.190 Angle : 0.624 9.671 122542 Z= 0.316 Chirality : 0.036 0.319 15721 Planarity : 0.004 0.081 6529 Dihedral : 24.822 179.452 40926 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.64 % Allowed : 21.54 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 2962 helix: 0.54 (0.18), residues: 901 sheet: -0.26 (0.21), residues: 600 loop : -1.42 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP W 296 HIS 0.015 0.001 HIS S 52 PHE 0.019 0.001 PHE Y 109 TYR 0.013 0.001 TYR V 225 ARG 0.012 0.000 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 345 time to evaluate : 3.426 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: C 54 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.9034 (mt0) REVERT: C 272 ARG cc_start: 0.8139 (tmm-80) cc_final: 0.7767 (tmm-80) REVERT: D 21 ASP cc_start: 0.8568 (m-30) cc_final: 0.8050 (m-30) REVERT: D 167 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8205 (pm20) REVERT: E 16 ASP cc_start: 0.8803 (m-30) cc_final: 0.8516 (p0) REVERT: F 71 SER cc_start: 0.7009 (t) cc_final: 0.6386 (m) REVERT: F 75 ASN cc_start: 0.6056 (t0) cc_final: 0.5414 (t0) REVERT: F 78 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6677 (pt0) REVERT: G 118 GLN cc_start: 0.9377 (tm-30) cc_final: 0.8779 (tm-30) REVERT: H 44 LYS cc_start: 0.9317 (ttmm) cc_final: 0.9098 (ttmm) REVERT: J 85 SER cc_start: 0.9060 (t) cc_final: 0.8709 (m) REVERT: L 49 ASP cc_start: 0.9325 (m-30) cc_final: 0.8928 (m-30) REVERT: L 56 ASP cc_start: 0.9362 (OUTLIER) cc_final: 0.9022 (m-30) REVERT: N 22 ASP cc_start: 0.9282 (m-30) cc_final: 0.8931 (m-30) REVERT: O 3 ASP cc_start: 0.8400 (t0) cc_final: 0.7823 (t0) REVERT: O 6 ASP cc_start: 0.8961 (m-30) cc_final: 0.8696 (m-30) REVERT: O 72 MET cc_start: 0.9283 (mtp) cc_final: 0.8829 (mmm) REVERT: O 89 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8381 (tp30) REVERT: P 31 ASP cc_start: 0.8806 (t0) cc_final: 0.8579 (t0) REVERT: P 39 ASN cc_start: 0.8932 (t0) cc_final: 0.8650 (t0) REVERT: P 40 MET cc_start: 0.9333 (mmt) cc_final: 0.8851 (mmm) REVERT: P 77 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8691 (pt0) REVERT: R 9 LEU cc_start: 0.7995 (tp) cc_final: 0.7707 (tt) REVERT: R 29 ARG cc_start: 0.8855 (mtm-85) cc_final: 0.8487 (ttm-80) REVERT: R 30 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8216 (t80) REVERT: T 29 GLU cc_start: 0.8179 (tm-30) cc_final: 0.6816 (mp0) REVERT: V 43 MET cc_start: 0.9201 (tpp) cc_final: 0.8966 (tmm) REVERT: V 95 GLN cc_start: 0.8406 (pp30) cc_final: 0.8112 (pp30) REVERT: V 102 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8813 (pp20) REVERT: V 108 PHE cc_start: 0.8693 (m-10) cc_final: 0.8329 (m-10) REVERT: V 112 ARG cc_start: 0.9292 (ptp-110) cc_final: 0.9019 (ptp90) REVERT: V 165 LYS cc_start: 0.8864 (tptp) cc_final: 0.8499 (pptt) REVERT: V 184 LEU cc_start: 0.8916 (tp) cc_final: 0.8697 (pt) REVERT: W 148 HIS cc_start: 0.3173 (m90) cc_final: 0.2151 (m90) REVERT: W 162 HIS cc_start: 0.8023 (m-70) cc_final: 0.7585 (m-70) REVERT: W 269 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: W 281 TYR cc_start: 0.8961 (m-80) cc_final: 0.8428 (m-80) REVERT: W 316 HIS cc_start: 0.8830 (m90) cc_final: 0.8241 (m90) REVERT: W 326 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8795 (mm) REVERT: Y 56 ASP cc_start: 0.5028 (OUTLIER) cc_final: 0.4717 (p0) REVERT: Y 126 LYS cc_start: 0.4528 (mmtt) cc_final: 0.3826 (tptp) outliers start: 90 outliers final: 66 residues processed: 405 average time/residue: 0.7244 time to fit residues: 512.5707 Evaluate side-chains 408 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 334 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 37 HIS Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 234 ILE Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain W residue 214 VAL Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain W residue 269 GLU Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 405 MET Chi-restraints excluded: chain W residue 426 THR Chi-restraints excluded: chain Y residue 56 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 147 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 102 optimal weight: 50.0000 chunk 30 optimal weight: 40.0000 chunk 438 optimal weight: 30.0000 chunk 512 optimal weight: 9.9990 chunk 372 optimal weight: 4.9990 chunk 404 optimal weight: 4.9990 chunk 269 optimal weight: 10.0000 chunk 530 optimal weight: 40.0000 chunk 140 optimal weight: 30.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 191 ASN ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN S 52 HIS V 203 GLN ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.071106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.045616 restraints weight = 303789.263| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.85 r_work: 0.2697 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 81869 Z= 0.409 Angle : 0.734 9.803 122542 Z= 0.369 Chirality : 0.042 0.339 15721 Planarity : 0.005 0.079 6529 Dihedral : 24.866 178.256 40926 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.67 % Rotamer: Outliers : 4.69 % Allowed : 21.29 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2962 helix: 0.57 (0.18), residues: 880 sheet: -0.36 (0.22), residues: 571 loop : -1.51 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP W 296 HIS 0.023 0.002 HIS S 52 PHE 0.016 0.002 PHE D 119 TYR 0.015 0.002 TYR C 83 ARG 0.007 0.001 ARG S 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 325 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 272 ARG cc_start: 0.8308 (tmm-80) cc_final: 0.7950 (tmm-80) REVERT: D 21 ASP cc_start: 0.8594 (m-30) cc_final: 0.8062 (m-30) REVERT: D 167 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8365 (pm20) REVERT: E 16 ASP cc_start: 0.8793 (m-30) cc_final: 0.8528 (p0) REVERT: F 71 SER cc_start: 0.7029 (t) cc_final: 0.6412 (m) REVERT: F 78 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6864 (pt0) REVERT: G 72 ASP cc_start: 0.8555 (m-30) cc_final: 0.8271 (m-30) REVERT: G 118 GLN cc_start: 0.9412 (tm-30) cc_final: 0.8825 (tm-30) REVERT: H 44 LYS cc_start: 0.9353 (ttmm) cc_final: 0.9124 (ttmm) REVERT: H 81 GLU cc_start: 0.9212 (pm20) cc_final: 0.8528 (pm20) REVERT: J 85 SER cc_start: 0.9117 (t) cc_final: 0.8681 (p) REVERT: J 86 ASP cc_start: 0.8919 (p0) cc_final: 0.8601 (p0) REVERT: J 95 GLN cc_start: 0.8917 (mt0) cc_final: 0.8703 (pt0) REVERT: K 105 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: L 49 ASP cc_start: 0.9342 (m-30) cc_final: 0.9014 (m-30) REVERT: L 56 ASP cc_start: 0.9382 (OUTLIER) cc_final: 0.9019 (m-30) REVERT: N 22 ASP cc_start: 0.9350 (m-30) cc_final: 0.9029 (m-30) REVERT: O 3 ASP cc_start: 0.8447 (t0) cc_final: 0.7899 (t0) REVERT: O 6 ASP cc_start: 0.9021 (m-30) cc_final: 0.8788 (m-30) REVERT: O 23 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8931 (mp0) REVERT: O 89 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8532 (tp30) REVERT: P 31 ASP cc_start: 0.8827 (t0) cc_final: 0.8543 (t0) REVERT: P 40 MET cc_start: 0.9280 (mmt) cc_final: 0.8836 (mmm) REVERT: R 17 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8741 (mmmm) REVERT: R 29 ARG cc_start: 0.8884 (mtm-85) cc_final: 0.8547 (mtt-85) REVERT: R 30 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8259 (t80) REVERT: T 29 GLU cc_start: 0.8083 (tm-30) cc_final: 0.6597 (mp0) REVERT: V 43 MET cc_start: 0.9224 (tpp) cc_final: 0.8932 (tmm) REVERT: V 108 PHE cc_start: 0.8750 (m-10) cc_final: 0.8251 (m-10) REVERT: V 112 ARG cc_start: 0.9306 (ptp-110) cc_final: 0.9079 (ptp-110) REVERT: V 165 LYS cc_start: 0.8915 (tptp) cc_final: 0.8551 (pptt) REVERT: W 148 HIS cc_start: 0.3478 (m90) cc_final: 0.2434 (m-70) REVERT: W 162 HIS cc_start: 0.8025 (m-70) cc_final: 0.7788 (m-70) REVERT: W 269 GLU cc_start: 0.7984 (mp0) cc_final: 0.7548 (pm20) REVERT: W 281 TYR cc_start: 0.8868 (m-80) cc_final: 0.8345 (m-80) REVERT: W 316 HIS cc_start: 0.8891 (m90) cc_final: 0.8257 (m90) REVERT: W 318 GLN cc_start: 0.9227 (mt0) cc_final: 0.8741 (tt0) REVERT: W 326 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8863 (mm) REVERT: W 365 ASP cc_start: 0.9126 (OUTLIER) cc_final: 0.8899 (t0) REVERT: Y 56 ASP cc_start: 0.5181 (OUTLIER) cc_final: 0.4813 (p0) outliers start: 116 outliers final: 86 residues processed: 412 average time/residue: 0.7373 time to fit residues: 534.0200 Evaluate side-chains 410 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 317 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 37 HIS Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 210 LEU Chi-restraints excluded: chain V residue 234 ILE Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 263 ILE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 242 THR Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 365 ASP Chi-restraints excluded: chain W residue 372 THR Chi-restraints excluded: chain W residue 405 MET Chi-restraints excluded: chain W residue 426 THR Chi-restraints excluded: chain Y residue 56 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 407 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 259 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 67 optimal weight: 40.0000 chunk 232 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 chunk 460 optimal weight: 0.7980 chunk 328 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN S 52 HIS V 203 GLN ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.072082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.046862 restraints weight = 303269.844| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.75 r_work: 0.2736 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 81869 Z= 0.254 Angle : 0.648 9.924 122542 Z= 0.328 Chirality : 0.038 0.333 15721 Planarity : 0.004 0.074 6529 Dihedral : 24.800 178.918 40926 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.16 % Allowed : 22.30 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 2962 helix: 0.68 (0.18), residues: 876 sheet: -0.34 (0.21), residues: 576 loop : -1.47 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP W 296 HIS 0.006 0.001 HIS L 29 PHE 0.012 0.001 PHE K 77 TYR 0.012 0.001 TYR F 110 ARG 0.005 0.000 ARG O 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 335 time to evaluate : 3.405 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: C 272 ARG cc_start: 0.8275 (tmm-80) cc_final: 0.7904 (tmm-80) REVERT: D 21 ASP cc_start: 0.8603 (m-30) cc_final: 0.8125 (m-30) REVERT: D 167 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: E 16 ASP cc_start: 0.8770 (m-30) cc_final: 0.8490 (p0) REVERT: F 71 SER cc_start: 0.7049 (t) cc_final: 0.6410 (m) REVERT: F 78 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6840 (pt0) REVERT: G 118 GLN cc_start: 0.9426 (tm-30) cc_final: 0.8831 (tm-30) REVERT: H 44 LYS cc_start: 0.9363 (ttmm) cc_final: 0.9140 (ttmm) REVERT: H 81 GLU cc_start: 0.9193 (pm20) cc_final: 0.8385 (pm20) REVERT: J 85 SER cc_start: 0.9066 (t) cc_final: 0.8731 (m) REVERT: J 95 GLN cc_start: 0.8854 (mt0) cc_final: 0.8583 (pt0) REVERT: K 105 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: L 49 ASP cc_start: 0.9314 (m-30) cc_final: 0.8975 (m-30) REVERT: L 56 ASP cc_start: 0.9338 (OUTLIER) cc_final: 0.9007 (m-30) REVERT: N 22 ASP cc_start: 0.9292 (m-30) cc_final: 0.8992 (m-30) REVERT: O 3 ASP cc_start: 0.8446 (t0) cc_final: 0.7887 (t0) REVERT: O 6 ASP cc_start: 0.9037 (m-30) cc_final: 0.8818 (m-30) REVERT: O 23 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8927 (mp0) REVERT: O 72 MET cc_start: 0.9248 (mtp) cc_final: 0.8875 (mmm) REVERT: O 89 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8473 (tp30) REVERT: P 31 ASP cc_start: 0.8856 (t0) cc_final: 0.8592 (t0) REVERT: P 77 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8730 (pt0) REVERT: R 29 ARG cc_start: 0.8865 (mtm-85) cc_final: 0.8507 (ttm-80) REVERT: R 30 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8267 (t80) REVERT: T 29 GLU cc_start: 0.8062 (tm-30) cc_final: 0.6668 (mp0) REVERT: V 43 MET cc_start: 0.9281 (tpp) cc_final: 0.9002 (tmm) REVERT: V 108 PHE cc_start: 0.8798 (m-10) cc_final: 0.8423 (m-10) REVERT: V 112 ARG cc_start: 0.9272 (ptp-110) cc_final: 0.9058 (ptp90) REVERT: V 165 LYS cc_start: 0.8956 (tptp) cc_final: 0.8578 (pptt) REVERT: W 148 HIS cc_start: 0.3336 (m90) cc_final: 0.2369 (m-70) REVERT: W 162 HIS cc_start: 0.8017 (m-70) cc_final: 0.7782 (m-70) REVERT: W 269 GLU cc_start: 0.7961 (mp0) cc_final: 0.7714 (pm20) REVERT: W 281 TYR cc_start: 0.8913 (m-80) cc_final: 0.8409 (m-80) REVERT: W 318 GLN cc_start: 0.9247 (mt0) cc_final: 0.8762 (tt0) REVERT: W 326 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8974 (mm) REVERT: Y 56 ASP cc_start: 0.5205 (OUTLIER) cc_final: 0.4842 (p0) REVERT: Y 137 MET cc_start: 0.8733 (pmm) cc_final: 0.8450 (tpt) outliers start: 103 outliers final: 82 residues processed: 413 average time/residue: 0.6799 time to fit residues: 491.7672 Evaluate side-chains 412 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 323 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 44 GLN Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 37 HIS Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 210 LEU Chi-restraints excluded: chain V residue 234 ILE Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 263 ILE Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 214 VAL Chi-restraints excluded: chain W residue 242 THR Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 405 MET Chi-restraints excluded: chain W residue 426 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 104 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 498 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 513 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 101 optimal weight: 50.0000 chunk 164 optimal weight: 10.0000 chunk 507 optimal weight: 5.9990 chunk 391 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 323 optimal weight: 7.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 HIS ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN S 52 HIS T 50 ASN V 105 GLN V 203 GLN ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.070882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.045583 restraints weight = 303789.531| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.77 r_work: 0.2697 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 81869 Z= 0.385 Angle : 0.720 10.083 122542 Z= 0.363 Chirality : 0.041 0.340 15721 Planarity : 0.005 0.074 6529 Dihedral : 24.834 178.314 40926 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 4.61 % Allowed : 22.10 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 2962 helix: 0.57 (0.18), residues: 887 sheet: -0.43 (0.21), residues: 580 loop : -1.57 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP W 296 HIS 0.011 0.001 HIS V 74 PHE 0.016 0.002 PHE D 119 TYR 0.015 0.002 TYR C 83 ARG 0.007 0.001 ARG F 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 323 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 272 ARG cc_start: 0.8284 (tmm-80) cc_final: 0.7911 (tmm-80) REVERT: D 21 ASP cc_start: 0.8561 (m-30) cc_final: 0.8116 (m-30) REVERT: D 167 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: F 71 SER cc_start: 0.7094 (t) cc_final: 0.6498 (m) REVERT: F 78 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6869 (pt0) REVERT: G 118 GLN cc_start: 0.9425 (tm-30) cc_final: 0.8793 (tm-30) REVERT: H 44 LYS cc_start: 0.9364 (ttmm) cc_final: 0.9129 (ttmm) REVERT: H 81 GLU cc_start: 0.9203 (pm20) cc_final: 0.8493 (pm20) REVERT: J 85 SER cc_start: 0.9101 (t) cc_final: 0.8676 (p) REVERT: J 86 ASP cc_start: 0.8891 (p0) cc_final: 0.8542 (p0) REVERT: K 105 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: L 49 ASP cc_start: 0.9327 (m-30) cc_final: 0.8996 (m-30) REVERT: L 56 ASP cc_start: 0.9346 (OUTLIER) cc_final: 0.8989 (m-30) REVERT: M 54 GLU cc_start: 0.9198 (tt0) cc_final: 0.8821 (pm20) REVERT: N 22 ASP cc_start: 0.9325 (m-30) cc_final: 0.9016 (m-30) REVERT: O 3 ASP cc_start: 0.8503 (t0) cc_final: 0.7966 (t0) REVERT: O 23 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8933 (mp0) REVERT: O 72 MET cc_start: 0.9271 (mtp) cc_final: 0.8784 (mmm) REVERT: O 89 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8478 (tp30) REVERT: P 31 ASP cc_start: 0.8849 (t0) cc_final: 0.8548 (t0) REVERT: R 8 ASP cc_start: 0.8187 (t0) cc_final: 0.7899 (t0) REVERT: R 29 ARG cc_start: 0.8888 (mtm-85) cc_final: 0.8557 (mtt-85) REVERT: R 30 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8208 (t80) REVERT: T 29 GLU cc_start: 0.7875 (tm-30) cc_final: 0.6447 (mp0) REVERT: V 43 MET cc_start: 0.9310 (tpp) cc_final: 0.9004 (tmm) REVERT: V 78 GLN cc_start: 0.7833 (mt0) cc_final: 0.7354 (mp10) REVERT: V 108 PHE cc_start: 0.8827 (m-10) cc_final: 0.7962 (m-10) REVERT: V 165 LYS cc_start: 0.8964 (tptp) cc_final: 0.8553 (pptt) REVERT: V 208 PHE cc_start: 0.8708 (t80) cc_final: 0.8464 (t80) REVERT: W 148 HIS cc_start: 0.3637 (m90) cc_final: 0.2716 (m90) REVERT: W 162 HIS cc_start: 0.8042 (m-70) cc_final: 0.7786 (m-70) REVERT: W 281 TYR cc_start: 0.8887 (m-80) cc_final: 0.8370 (m-80) REVERT: W 326 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8946 (mm) outliers start: 114 outliers final: 97 residues processed: 407 average time/residue: 0.6872 time to fit residues: 491.1443 Evaluate side-chains 416 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 314 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 44 GLN Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 37 HIS Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 210 LEU Chi-restraints excluded: chain V residue 234 ILE Chi-restraints excluded: chain V residue 263 ILE Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 214 VAL Chi-restraints excluded: chain W residue 242 THR Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 372 THR Chi-restraints excluded: chain W residue 426 THR Chi-restraints excluded: chain Y residue 56 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 370 optimal weight: 0.8980 chunk 513 optimal weight: 2.9990 chunk 411 optimal weight: 8.9990 chunk 318 optimal weight: 9.9990 chunk 447 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 416 optimal weight: 0.6980 chunk 409 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN S 52 HIS V 105 GLN V 203 GLN ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.072628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.047575 restraints weight = 303214.351| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.73 r_work: 0.2761 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 81869 Z= 0.178 Angle : 0.625 10.901 122542 Z= 0.317 Chirality : 0.036 0.331 15721 Planarity : 0.004 0.069 6529 Dihedral : 24.769 179.706 40926 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.39 % Allowed : 23.47 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 2962 helix: 0.77 (0.18), residues: 877 sheet: -0.34 (0.21), residues: 599 loop : -1.45 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP W 296 HIS 0.011 0.001 HIS V 74 PHE 0.014 0.001 PHE V 108 TYR 0.013 0.001 TYR F 110 ARG 0.008 0.000 ARG V 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 329 time to evaluate : 3.395 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: C 272 ARG cc_start: 0.8193 (tmm-80) cc_final: 0.7812 (tmm-80) REVERT: D 21 ASP cc_start: 0.8594 (m-30) cc_final: 0.8154 (m-30) REVERT: D 167 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: E 16 ASP cc_start: 0.8740 (m-30) cc_final: 0.8494 (p0) REVERT: F 71 SER cc_start: 0.7167 (t) cc_final: 0.6571 (m) REVERT: F 78 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6749 (pt0) REVERT: G 118 GLN cc_start: 0.9403 (tm-30) cc_final: 0.8780 (tm-30) REVERT: H 44 LYS cc_start: 0.9384 (ttmm) cc_final: 0.9161 (ttmm) REVERT: J 85 SER cc_start: 0.9034 (t) cc_final: 0.8724 (m) REVERT: K 105 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: L 49 ASP cc_start: 0.9313 (m-30) cc_final: 0.8927 (m-30) REVERT: L 56 ASP cc_start: 0.9343 (OUTLIER) cc_final: 0.9002 (m-30) REVERT: M 54 GLU cc_start: 0.9114 (tt0) cc_final: 0.8782 (pm20) REVERT: N 22 ASP cc_start: 0.9295 (m-30) cc_final: 0.9021 (m-30) REVERT: O 3 ASP cc_start: 0.8634 (t0) cc_final: 0.8146 (t0) REVERT: O 23 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8897 (mp0) REVERT: O 72 MET cc_start: 0.9245 (mtp) cc_final: 0.8885 (mmm) REVERT: O 89 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8455 (tp30) REVERT: P 31 ASP cc_start: 0.8833 (t0) cc_final: 0.8615 (t0) REVERT: P 40 MET cc_start: 0.9376 (mmt) cc_final: 0.8920 (mmp) REVERT: P 77 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8765 (pt0) REVERT: R 29 ARG cc_start: 0.8881 (mtm-85) cc_final: 0.8533 (ttm-80) REVERT: R 30 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8205 (t80) REVERT: T 29 GLU cc_start: 0.8117 (tm-30) cc_final: 0.6702 (mp0) REVERT: V 43 MET cc_start: 0.9339 (tpp) cc_final: 0.9060 (tmm) REVERT: V 78 GLN cc_start: 0.7835 (mt0) cc_final: 0.7371 (mp10) REVERT: V 102 GLU cc_start: 0.8957 (pp20) cc_final: 0.8694 (pp20) REVERT: V 165 LYS cc_start: 0.8997 (tptp) cc_final: 0.8603 (pptt) REVERT: V 208 PHE cc_start: 0.8629 (t80) cc_final: 0.8407 (t80) REVERT: W 148 HIS cc_start: 0.3572 (m90) cc_final: 0.2693 (m90) REVERT: W 162 HIS cc_start: 0.8038 (m-70) cc_final: 0.7769 (m-70) REVERT: W 269 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: W 281 TYR cc_start: 0.8875 (m-80) cc_final: 0.8373 (m-80) REVERT: W 318 GLN cc_start: 0.9243 (mt0) cc_final: 0.8820 (tt0) outliers start: 84 outliers final: 68 residues processed: 386 average time/residue: 0.6912 time to fit residues: 463.8604 Evaluate side-chains 398 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 324 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 44 GLN Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 37 HIS Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 210 LEU Chi-restraints excluded: chain V residue 234 ILE Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain W residue 269 GLU Chi-restraints excluded: chain W residue 426 THR Chi-restraints excluded: chain Y residue 56 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 482 optimal weight: 10.0000 chunk 197 optimal weight: 40.0000 chunk 279 optimal weight: 9.9990 chunk 358 optimal weight: 9.9990 chunk 379 optimal weight: 5.9990 chunk 356 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 520 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 386 optimal weight: 0.9980 chunk 269 optimal weight: 9.9990 overall best weight: 5.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN L 72 ASN R 4 ASN S 52 HIS V 203 GLN ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.071515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.046340 restraints weight = 302002.585| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.72 r_work: 0.2723 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 81869 Z= 0.290 Angle : 0.665 10.654 122542 Z= 0.336 Chirality : 0.038 0.337 15721 Planarity : 0.004 0.068 6529 Dihedral : 24.745 178.643 40926 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.56 % Rotamer: Outliers : 3.23 % Allowed : 23.84 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 2962 helix: 0.73 (0.18), residues: 884 sheet: -0.33 (0.21), residues: 585 loop : -1.48 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP W 296 HIS 0.009 0.001 HIS V 74 PHE 0.012 0.001 PHE K 77 TYR 0.014 0.001 TYR C 83 ARG 0.009 0.000 ARG R 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 322 time to evaluate : 3.396 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: C 272 ARG cc_start: 0.8209 (tmm-80) cc_final: 0.7812 (tmm-80) REVERT: D 21 ASP cc_start: 0.8599 (m-30) cc_final: 0.8163 (m-30) REVERT: D 167 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: F 71 SER cc_start: 0.7146 (t) cc_final: 0.6558 (m) REVERT: F 78 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6850 (pt0) REVERT: G 118 GLN cc_start: 0.9426 (tm-30) cc_final: 0.8832 (tm-30) REVERT: H 44 LYS cc_start: 0.9377 (ttmm) cc_final: 0.9137 (ttmm) REVERT: H 81 GLU cc_start: 0.9201 (pm20) cc_final: 0.8493 (pm20) REVERT: J 85 SER cc_start: 0.9100 (t) cc_final: 0.8807 (m) REVERT: K 105 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: L 49 ASP cc_start: 0.9311 (m-30) cc_final: 0.8936 (m-30) REVERT: L 56 ASP cc_start: 0.9337 (OUTLIER) cc_final: 0.9002 (m-30) REVERT: M 54 GLU cc_start: 0.9153 (tt0) cc_final: 0.8784 (pm20) REVERT: N 22 ASP cc_start: 0.9313 (m-30) cc_final: 0.9035 (m-30) REVERT: O 3 ASP cc_start: 0.8584 (t0) cc_final: 0.8225 (t0) REVERT: O 23 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8897 (mp0) REVERT: O 72 MET cc_start: 0.9269 (mtp) cc_final: 0.8866 (mmm) REVERT: O 89 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8459 (tp30) REVERT: P 31 ASP cc_start: 0.8865 (t0) cc_final: 0.8615 (t0) REVERT: P 77 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8756 (pt0) REVERT: R 29 ARG cc_start: 0.8876 (mtm-85) cc_final: 0.8587 (ttm-80) REVERT: R 30 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8259 (t80) REVERT: S 5 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8812 (mt-10) REVERT: T 29 GLU cc_start: 0.8039 (tm-30) cc_final: 0.6683 (mp0) REVERT: V 43 MET cc_start: 0.9353 (tpp) cc_final: 0.9045 (tmm) REVERT: V 78 GLN cc_start: 0.7814 (mt0) cc_final: 0.7368 (mp10) REVERT: V 102 GLU cc_start: 0.8956 (pp20) cc_final: 0.8684 (pp20) REVERT: V 165 LYS cc_start: 0.9035 (tptp) cc_final: 0.8613 (pptt) REVERT: V 208 PHE cc_start: 0.8658 (t80) cc_final: 0.8425 (t80) REVERT: W 148 HIS cc_start: 0.3685 (m90) cc_final: 0.2783 (m90) REVERT: W 162 HIS cc_start: 0.7964 (m-70) cc_final: 0.7660 (m-70) REVERT: W 281 TYR cc_start: 0.8876 (m-80) cc_final: 0.8379 (m-80) REVERT: W 318 GLN cc_start: 0.9193 (mt0) cc_final: 0.8726 (tt0) REVERT: Y 121 MET cc_start: 0.5850 (mmt) cc_final: 0.5553 (mmt) outliers start: 80 outliers final: 70 residues processed: 380 average time/residue: 0.6894 time to fit residues: 457.3656 Evaluate side-chains 394 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 319 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 68 ASN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 44 GLN Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 37 HIS Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 210 LEU Chi-restraints excluded: chain V residue 234 ILE Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain W residue 426 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 382 optimal weight: 5.9990 chunk 351 optimal weight: 20.0000 chunk 368 optimal weight: 0.8980 chunk 43 optimal weight: 30.0000 chunk 456 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 245 optimal weight: 0.8980 chunk 400 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN L 72 ASN S 52 HIS ** V 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 203 GLN ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.072422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.047390 restraints weight = 302432.697| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.70 r_work: 0.2755 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 81869 Z= 0.185 Angle : 0.624 10.907 122542 Z= 0.316 Chirality : 0.036 0.333 15721 Planarity : 0.004 0.068 6529 Dihedral : 24.719 179.506 40926 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.87 % Allowed : 24.36 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 2962 helix: 0.78 (0.18), residues: 877 sheet: -0.25 (0.22), residues: 592 loop : -1.42 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP W 296 HIS 0.009 0.001 HIS V 74 PHE 0.012 0.001 PHE K 77 TYR 0.013 0.001 TYR F 110 ARG 0.007 0.000 ARG I 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43718.76 seconds wall clock time: 748 minutes 26.53 seconds (44906.53 seconds total)