Starting phenix.real_space_refine on Sun Jan 26 11:32:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bss_44871/01_2025/9bss_44871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bss_44871/01_2025/9bss_44871.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/9bss_44871/01_2025/9bss_44871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bss_44871/01_2025/9bss_44871.map" model { file = "/net/cci-nas-00/data/ceres_data/9bss_44871/01_2025/9bss_44871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bss_44871/01_2025/9bss_44871.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= 0.005 sd= 0.031 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 2693 5.49 5 S 69 5.16 5 C 40718 2.51 5 N 15097 2.21 5 O 23032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 81609 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 55237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2572, 55237 Classifications: {'RNA': 2572} Modifications used: {'rna2p_pur': 274, 'rna2p_pyr': 151, 'rna3p_pur': 1220, 'rna3p_pyr': 927} Link IDs: {'rna2p': 425, 'rna3p': 2146} Chain breaks: 16 Chain: "B" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2395 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 11, 'rna3p_pur': 52, 'rna3p_pyr': 41} Link IDs: {'rna2p': 19, 'rna3p': 92} 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: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1551 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 197} 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: "Q" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 423 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 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: 33.71, per 1000 atoms: 0.41 Number of scatterers: 81609 At special positions: 0 Unit cell: (191.52, 235.98, 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 2693 15.00 O 23032 8.00 N 15097 7.00 C 40718 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 41378 O5' C A2206 .*. O " rejected from bonding due to valence issues. Atom "ATOM 40819 O4' A A2152 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.07 Conformation dependent library (CDL) restraints added in 3.4 seconds 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5664 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 39 sheets defined 31.4% alpha, 18.6% beta 787 base pairs and 1273 stacking pairs defined. Time for finding SS restraints: 29.92 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: 3.957A 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 'Q' and resid 38 through 39 Processing sheet with id=AD3, first strand: chain 'Q' and resid 61 through 62 Processing sheet with id=AD4, first strand: chain 'S' and resid 34 through 38 Processing sheet with id=AD5, first strand: chain 'T' and resid 48 through 49 Processing sheet with id=AD6, 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=AD7, 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=AD8, 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=AD9, 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=AE1, 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=AE2, 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=AE3, first strand: chain 'Y' and resid 75 through 76 807 hydrogen bonds defined for protein. 2238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2007 hydrogen bonds 3252 hydrogen bond angles 0 basepair planarities 787 basepair parallelities 1273 stacking parallelities Total time for adding SS restraints: 119.68 Time building geometry restraints manager: 18.26 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: 12184 1.33 - 1.45: 37461 1.45 - 1.57: 33685 1.57 - 1.69: 5361 1.69 - 1.81: 135 Bond restraints: 88826 Sorted by residual: bond pdb=" N PRO Q 91 " pdb=" CD PRO Q 91 " ideal model delta sigma weight residual 1.473 1.550 -0.077 1.40e-02 5.10e+03 3.03e+01 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 ... (remaining 88821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 132428 3.24 - 6.48: 795 6.48 - 9.72: 61 9.72 - 12.97: 10 12.97 - 16.21: 3 Bond angle restraints: 133297 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 133292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 48908 35.93 - 71.85: 6933 71.85 - 107.78: 883 107.78 - 143.71: 48 143.71 - 179.63: 43 Dihedral angle restraints: 56815 sinusoidal: 48021 harmonic: 8794 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 56812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 16212 0.080 - 0.160: 843 0.160 - 0.240: 75 0.240 - 0.321: 9 0.321 - 0.401: 2 Chirality restraints: 17141 Sorted by residual: chirality pdb=" C1' C A2313 " pdb=" O4' C A2313 " pdb=" C2' C A2313 " pdb=" N1 C A2313 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C1' A A 200 " pdb=" O4' A A 200 " pdb=" C2' A A 200 " pdb=" N9 A A 200 " both_signs ideal model delta sigma weight residual False 2.46 2.11 0.35 2.00e-01 2.50e+01 2.98e+00 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 ... (remaining 17138 not shown) Planarity restraints: 6884 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=" C TYR Q 54 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO Q 55 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO Q 55 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO Q 55 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C A2313 " -0.046 2.00e-02 2.50e+03 2.42e-02 1.32e+01 pdb=" N1 C A2313 " 0.053 2.00e-02 2.50e+03 pdb=" C2 C A2313 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C A2313 " 0.007 2.00e-02 2.50e+03 pdb=" N3 C A2313 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C A2313 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C A2313 " -0.015 2.00e-02 2.50e+03 pdb=" C5 C A2313 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C A2313 " 0.006 2.00e-02 2.50e+03 ... (remaining 6881 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 8 1.80 - 2.58: 861 2.58 - 3.35: 94423 3.35 - 4.13: 250457 4.13 - 4.90: 366712 Nonbonded interactions: 712461 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 712456 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: 7.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 2.790 Check model and map are aligned: 0.510 Set scattering table: 0.600 Process input model: 238.570 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: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 253.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 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 88826 Z= 0.210 Angle : 0.679 16.207 133297 Z= 0.358 Chirality : 0.038 0.401 17141 Planarity : 0.005 0.103 6884 Dihedral : 25.312 179.632 51151 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 0.68 % Allowed : 20.22 % Favored : 79.10 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: 3026 helix: 0.17 (0.19), residues: 870 sheet: -0.39 (0.22), residues: 532 loop : -1.55 (0.14), residues: 1624 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 0.016 0.000 ARG Q 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 291 time to evaluate : 3.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 148 ASN cc_start: 0.8785 (m110) cc_final: 0.8537 (m-40) REVERT: G 118 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8841 (tm-30) REVERT: K 115 GLU cc_start: 0.8173 (tp30) cc_final: 0.7736 (tp30) REVERT: M 2 TYR cc_start: 0.8355 (t80) cc_final: 0.8087 (t80) REVERT: R 15 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8970 (tm-30) REVERT: T 16 ARG cc_start: 0.9486 (OUTLIER) cc_final: 0.8351 (ttp80) REVERT: T 36 MET cc_start: 0.7974 (tpp) cc_final: 0.7705 (tpp) REVERT: V 4 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7559 (tm-30) REVERT: Y 57 GLN cc_start: 0.2658 (OUTLIER) cc_final: 0.1919 (pp30) REVERT: Y 78 PHE cc_start: 0.6139 (m-10) cc_final: 0.5859 (m-80) outliers start: 17 outliers final: 1 residues processed: 304 average time/residue: 0.7861 time to fit residues: 406.9594 Evaluate side-chains 262 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 259 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain Y residue 57 GLN Chi-restraints excluded: chain Y residue 130 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 477 optimal weight: 0.0000 chunk 429 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 289 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 443 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 chunk 330 optimal weight: 6.9990 chunk 513 optimal weight: 10.0000 overall best weight: 5.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 4 ASN W 312 ASN W 349 ASN Y 57 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.067407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.042824 restraints weight = 376095.065| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.54 r_work: 0.2781 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 88826 Z= 0.266 Angle : 0.682 9.869 133297 Z= 0.343 Chirality : 0.039 0.415 17141 Planarity : 0.005 0.069 6884 Dihedral : 25.677 179.437 45207 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.95 % Allowed : 19.19 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -1.06 (0.15), residues: 3026 helix: 0.31 (0.18), residues: 909 sheet: -0.38 (0.22), residues: 534 loop : -1.43 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP W 296 HIS 0.018 0.001 HIS Y 172 PHE 0.024 0.001 PHE Y 111 TYR 0.020 0.002 TYR W 131 ARG 0.006 0.000 ARG Y 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 266 time to evaluate : 3.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.8968 (mm110) cc_final: 0.8734 (mm110) REVERT: G 61 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: G 72 ASP cc_start: 0.8763 (m-30) cc_final: 0.8440 (m-30) REVERT: M 2 TYR cc_start: 0.8367 (t80) cc_final: 0.8166 (t80) REVERT: Q 48 GLN cc_start: 0.6969 (pt0) cc_final: 0.6547 (pm20) REVERT: T 36 MET cc_start: 0.7852 (tpp) cc_final: 0.7610 (tpp) REVERT: V 69 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8765 (tm-30) REVERT: V 166 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: W 222 GLN cc_start: 0.8882 (mp10) cc_final: 0.8310 (tm-30) REVERT: W 328 MET cc_start: 0.8104 (pmm) cc_final: 0.7483 (pmm) REVERT: Y 78 PHE cc_start: 0.7464 (m-10) cc_final: 0.6672 (m-80) REVERT: Y 101 ILE cc_start: 0.8587 (mp) cc_final: 0.8213 (tt) outliers start: 49 outliers final: 26 residues processed: 309 average time/residue: 0.7744 time to fit residues: 415.4004 Evaluate side-chains 281 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain V residue 166 GLU Chi-restraints excluded: chain V residue 260 THR Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain Y residue 130 VAL Chi-restraints excluded: chain Y residue 131 LEU Chi-restraints excluded: chain Y residue 139 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 210 optimal weight: 50.0000 chunk 151 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 chunk 505 optimal weight: 3.9990 chunk 217 optimal weight: 40.0000 chunk 509 optimal weight: 30.0000 chunk 530 optimal weight: 20.0000 chunk 372 optimal weight: 9.9990 chunk 512 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 441 optimal weight: 9.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 50 ASN Y 55 ASN ** Y 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.066381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.041610 restraints weight = 375046.469| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.61 r_work: 0.2726 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 88826 Z= 0.378 Angle : 0.740 10.872 133297 Z= 0.372 Chirality : 0.041 0.453 17141 Planarity : 0.005 0.065 6884 Dihedral : 25.632 179.430 45200 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.10 % Allowed : 18.79 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -1.12 (0.15), residues: 3026 helix: 0.34 (0.18), residues: 907 sheet: -0.41 (0.22), residues: 523 loop : -1.52 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 296 HIS 0.006 0.001 HIS L 29 PHE 0.013 0.001 PHE Y 111 TYR 0.016 0.002 TYR W 246 ARG 0.008 0.001 ARG Y 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 258 time to evaluate : 3.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.8988 (mm110) cc_final: 0.8751 (mm110) REVERT: F 10 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6602 (mm-30) REVERT: G 61 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8159 (pm20) REVERT: G 72 ASP cc_start: 0.8821 (m-30) cc_final: 0.8479 (m-30) REVERT: H 37 ASP cc_start: 0.8821 (m-30) cc_final: 0.8519 (m-30) REVERT: H 47 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7527 (t) REVERT: I 90 GLU cc_start: 0.8942 (tp30) cc_final: 0.8657 (tp30) REVERT: M 36 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: P 31 ASP cc_start: 0.8994 (t70) cc_final: 0.8532 (t0) REVERT: Q 48 GLN cc_start: 0.7004 (pt0) cc_final: 0.6614 (pm20) REVERT: Q 76 LYS cc_start: 0.6785 (mmmt) cc_final: 0.6418 (tmmt) REVERT: S 5 GLU cc_start: 0.8426 (mp0) cc_final: 0.7417 (mp0) REVERT: T 16 ARG cc_start: 0.9568 (OUTLIER) cc_final: 0.8615 (ttp80) REVERT: T 27 MET cc_start: 0.8422 (mmm) cc_final: 0.8072 (tpp) REVERT: V 69 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8745 (tm-30) REVERT: W 222 GLN cc_start: 0.8754 (mp10) cc_final: 0.8429 (tm-30) REVERT: W 326 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8694 (mm) REVERT: Y 101 ILE cc_start: 0.8839 (mp) cc_final: 0.8463 (tt) REVERT: Y 104 ILE cc_start: 0.8309 (mm) cc_final: 0.8046 (mm) outliers start: 78 outliers final: 43 residues processed: 327 average time/residue: 0.8455 time to fit residues: 484.8801 Evaluate side-chains 295 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 95 GLN Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 372 THR Chi-restraints excluded: chain Y residue 130 VAL Chi-restraints excluded: chain Y residue 139 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 232 optimal weight: 10.0000 chunk 242 optimal weight: 30.0000 chunk 479 optimal weight: 7.9990 chunk 103 optimal weight: 50.0000 chunk 519 optimal weight: 40.0000 chunk 210 optimal weight: 50.0000 chunk 419 optimal weight: 8.9990 chunk 146 optimal weight: 30.0000 chunk 379 optimal weight: 3.9990 chunk 405 optimal weight: 7.9990 chunk 258 optimal weight: 50.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.066437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.041748 restraints weight = 375753.301| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.60 r_work: 0.2735 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 88826 Z= 0.358 Angle : 0.718 10.613 133297 Z= 0.361 Chirality : 0.041 0.455 17141 Planarity : 0.005 0.063 6884 Dihedral : 25.573 179.740 45200 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.06 % Allowed : 19.75 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -1.09 (0.15), residues: 3026 helix: 0.46 (0.18), residues: 894 sheet: -0.37 (0.22), residues: 530 loop : -1.57 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 296 HIS 0.006 0.001 HIS L 29 PHE 0.011 0.001 PHE Y 111 TYR 0.015 0.002 TYR W 246 ARG 0.004 0.000 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 254 time to evaluate : 3.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.8968 (mm110) cc_final: 0.8713 (mm110) REVERT: C 225 MET cc_start: 0.6019 (mtp) cc_final: 0.5736 (mtp) REVERT: G 61 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8148 (pm20) REVERT: G 72 ASP cc_start: 0.8829 (m-30) cc_final: 0.8485 (m-30) REVERT: H 47 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7526 (t) REVERT: I 95 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6686 (tm) REVERT: J 102 MET cc_start: 0.9084 (mtp) cc_final: 0.8690 (mtp) REVERT: M 28 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8166 (tm-30) REVERT: M 31 GLU cc_start: 0.8643 (pm20) cc_final: 0.8336 (pm20) REVERT: M 36 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7845 (mm-30) REVERT: P 31 ASP cc_start: 0.9043 (t70) cc_final: 0.8566 (t0) REVERT: Q 48 GLN cc_start: 0.6945 (pt0) cc_final: 0.6542 (pm20) REVERT: Q 76 LYS cc_start: 0.7033 (mmmt) cc_final: 0.6569 (tmmt) REVERT: R 30 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8623 (t80) REVERT: S 9 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9186 (ptpp) REVERT: T 16 ARG cc_start: 0.9569 (OUTLIER) cc_final: 0.8598 (ttp80) REVERT: V 165 LYS cc_start: 0.8859 (tppt) cc_final: 0.8612 (tptp) REVERT: W 222 GLN cc_start: 0.8720 (mp10) cc_final: 0.8421 (tm-30) REVERT: W 318 GLN cc_start: 0.9156 (mt0) cc_final: 0.8579 (tt0) REVERT: W 326 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8637 (mm) REVERT: Y 121 MET cc_start: 0.7432 (tpt) cc_final: 0.7113 (mmp) outliers start: 77 outliers final: 51 residues processed: 322 average time/residue: 0.7102 time to fit residues: 397.6871 Evaluate side-chains 301 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 25 VAL 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 187 VAL Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 148 ASN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 136 LEU Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 424 GLU Chi-restraints excluded: chain Y residue 130 VAL Chi-restraints excluded: chain Y residue 131 LEU Chi-restraints excluded: chain Y residue 173 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 226 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 148 optimal weight: 40.0000 chunk 528 optimal weight: 1.9990 chunk 505 optimal weight: 20.0000 chunk 332 optimal weight: 30.0000 chunk 477 optimal weight: 40.0000 chunk 285 optimal weight: 9.9990 chunk 309 optimal weight: 5.9990 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 ASN V 69 GLN ** W 148 HIS ** 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 = 0.3589 r_free = 0.3589 target = 0.066187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.041639 restraints weight = 369739.528| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.58 r_work: 0.2732 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 88826 Z= 0.353 Angle : 0.722 10.851 133297 Z= 0.363 Chirality : 0.041 0.461 17141 Planarity : 0.005 0.072 6884 Dihedral : 25.534 179.965 45200 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.38 % Allowed : 20.54 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -1.10 (0.15), residues: 3026 helix: 0.40 (0.18), residues: 906 sheet: -0.42 (0.22), residues: 538 loop : -1.54 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP W 296 HIS 0.006 0.001 HIS L 29 PHE 0.015 0.001 PHE V 212 TYR 0.013 0.001 TYR C 83 ARG 0.005 0.000 ARG Y 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 257 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.8973 (mm110) cc_final: 0.8702 (mm110) REVERT: F 10 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6586 (mm-30) REVERT: F 59 GLN cc_start: 0.8351 (tp40) cc_final: 0.7338 (mp10) REVERT: G 61 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: G 72 ASP cc_start: 0.8828 (m-30) cc_final: 0.8484 (m-30) REVERT: G 118 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.9196 (tm-30) REVERT: H 47 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7554 (t) REVERT: I 95 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6472 (tm) REVERT: J 102 MET cc_start: 0.9069 (mtp) cc_final: 0.8663 (mtp) REVERT: M 28 GLU cc_start: 0.8681 (tm-30) cc_final: 0.7681 (tm-30) REVERT: M 31 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8238 (pm20) REVERT: M 36 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: P 31 ASP cc_start: 0.9016 (t70) cc_final: 0.8563 (t0) REVERT: Q 48 GLN cc_start: 0.6847 (pt0) cc_final: 0.6485 (pm20) REVERT: Q 76 LYS cc_start: 0.7048 (mmmt) cc_final: 0.6523 (tmmt) REVERT: R 30 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8649 (t80) REVERT: S 5 GLU cc_start: 0.8564 (mp0) cc_final: 0.8027 (mp0) REVERT: T 16 ARG cc_start: 0.9575 (OUTLIER) cc_final: 0.8624 (ttp80) REVERT: T 27 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7916 (tpp) REVERT: V 69 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8830 (tm-30) REVERT: V 165 LYS cc_start: 0.8847 (tppt) cc_final: 0.8611 (tptp) REVERT: W 222 GLN cc_start: 0.8686 (mp10) cc_final: 0.8444 (tm-30) REVERT: W 326 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8672 (mm) REVERT: Y 121 MET cc_start: 0.7563 (tpt) cc_final: 0.7140 (mmp) outliers start: 85 outliers final: 58 residues processed: 329 average time/residue: 0.6798 time to fit residues: 390.5819 Evaluate side-chains 315 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 245 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 136 LEU Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 372 THR Chi-restraints excluded: chain Y residue 131 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 158 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 102 optimal weight: 30.0000 chunk 242 optimal weight: 40.0000 chunk 75 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 546 optimal weight: 5.9990 chunk 407 optimal weight: 4.9990 chunk 269 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 69 GLN W 74 GLN ** W 148 HIS ** 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 = 0.3586 r_free = 0.3586 target = 0.066065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.041492 restraints weight = 371118.266| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.60 r_work: 0.2729 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 88826 Z= 0.368 Angle : 0.727 10.891 133297 Z= 0.366 Chirality : 0.041 0.459 17141 Planarity : 0.005 0.062 6884 Dihedral : 25.520 179.943 45199 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.73 % Allowed : 21.41 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -1.12 (0.15), residues: 3026 helix: 0.45 (0.18), residues: 889 sheet: -0.43 (0.22), residues: 535 loop : -1.58 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP W 296 HIS 0.006 0.001 HIS L 29 PHE 0.012 0.001 PHE Y 94 TYR 0.013 0.001 TYR C 83 ARG 0.004 0.000 ARG O 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 251 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.8987 (mm110) cc_final: 0.8716 (mm110) REVERT: F 10 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6688 (mm-30) REVERT: F 59 GLN cc_start: 0.8408 (tp40) cc_final: 0.7407 (mp10) REVERT: G 61 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: G 72 ASP cc_start: 0.8827 (m-30) cc_final: 0.8487 (m-30) REVERT: G 118 GLN cc_start: 0.9477 (OUTLIER) cc_final: 0.9194 (tm-30) REVERT: H 47 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7560 (t) REVERT: I 90 GLU cc_start: 0.8956 (tp30) cc_final: 0.8624 (tp30) REVERT: I 95 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6668 (tm) REVERT: J 102 MET cc_start: 0.9065 (mtp) cc_final: 0.8648 (mtp) REVERT: M 28 GLU cc_start: 0.8709 (tm-30) cc_final: 0.7624 (tm-30) REVERT: M 31 GLU cc_start: 0.8676 (pm20) cc_final: 0.8206 (pm20) REVERT: M 36 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7814 (mm-30) REVERT: P 31 ASP cc_start: 0.9002 (t70) cc_final: 0.8538 (t0) REVERT: Q 48 GLN cc_start: 0.6682 (pt0) cc_final: 0.6386 (pm20) REVERT: Q 76 LYS cc_start: 0.7087 (mmmt) cc_final: 0.6558 (tmmt) REVERT: R 30 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8656 (t80) REVERT: S 5 GLU cc_start: 0.8569 (mp0) cc_final: 0.8352 (mp0) REVERT: T 16 ARG cc_start: 0.9578 (OUTLIER) cc_final: 0.8619 (ttp80) REVERT: T 27 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8037 (tpp) REVERT: V 165 LYS cc_start: 0.8847 (tppt) cc_final: 0.8598 (tptp) REVERT: W 222 GLN cc_start: 0.8616 (mp10) cc_final: 0.8391 (tm-30) REVERT: W 318 GLN cc_start: 0.9189 (mt0) cc_final: 0.8559 (tt0) REVERT: W 326 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8698 (mm) outliers start: 94 outliers final: 67 residues processed: 334 average time/residue: 0.6606 time to fit residues: 384.5343 Evaluate side-chains 320 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 243 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 27 MET 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 22 LYS Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 136 LEU Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 71 GLN Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 372 THR Chi-restraints excluded: chain W residue 424 GLU Chi-restraints excluded: chain Y residue 131 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 37 optimal weight: 10.0000 chunk 267 optimal weight: 50.0000 chunk 545 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 501 optimal weight: 9.9990 chunk 40 optimal weight: 40.0000 chunk 257 optimal weight: 50.0000 chunk 283 optimal weight: 8.9990 chunk 488 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- 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** ** V 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.065670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.041028 restraints weight = 376231.301| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 1.66 r_work: 0.2711 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 88826 Z= 0.445 Angle : 0.776 11.458 133297 Z= 0.389 Chirality : 0.044 0.466 17141 Planarity : 0.005 0.064 6884 Dihedral : 25.553 179.961 45199 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.89 % Allowed : 21.26 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 3026 helix: 0.30 (0.18), residues: 892 sheet: -0.48 (0.22), residues: 532 loop : -1.62 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP W 296 HIS 0.008 0.001 HIS F 39 PHE 0.013 0.001 PHE Y 94 TYR 0.015 0.002 TYR C 83 ARG 0.004 0.000 ARG O 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 247 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.8983 (mm110) cc_final: 0.8731 (mm110) REVERT: F 10 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6720 (mm-30) REVERT: F 59 GLN cc_start: 0.8393 (tp40) cc_final: 0.7454 (pm20) REVERT: G 61 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: G 72 ASP cc_start: 0.8884 (m-30) cc_final: 0.8565 (m-30) REVERT: H 47 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7660 (t) REVERT: I 90 GLU cc_start: 0.8970 (tp30) cc_final: 0.8634 (tp30) REVERT: I 95 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6686 (tm) REVERT: J 102 MET cc_start: 0.9070 (mtp) cc_final: 0.8659 (mtp) REVERT: M 28 GLU cc_start: 0.8728 (tm-30) cc_final: 0.7647 (tm-30) REVERT: M 31 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: M 36 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7845 (mm-30) REVERT: P 31 ASP cc_start: 0.9002 (t70) cc_final: 0.8530 (t0) REVERT: R 30 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8645 (t80) REVERT: S 5 GLU cc_start: 0.8550 (mp0) cc_final: 0.7401 (mp0) REVERT: T 16 ARG cc_start: 0.9579 (OUTLIER) cc_final: 0.8596 (ttp80) REVERT: T 27 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8205 (tpp) REVERT: V 165 LYS cc_start: 0.8864 (tppt) cc_final: 0.8583 (tptp) REVERT: W 318 GLN cc_start: 0.9192 (mt0) cc_final: 0.8579 (tt0) REVERT: W 326 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8718 (mm) outliers start: 98 outliers final: 76 residues processed: 333 average time/residue: 0.6489 time to fit residues: 375.5803 Evaluate side-chains 327 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 241 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 27 MET 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 31 VAL Chi-restraints excluded: chain V residue 136 LEU Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 71 GLN Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 372 THR Chi-restraints excluded: chain Y residue 131 LEU Chi-restraints excluded: chain Y residue 139 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 310 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 521 optimal weight: 4.9990 chunk 188 optimal weight: 50.0000 chunk 299 optimal weight: 6.9990 chunk 351 optimal weight: 3.9990 chunk 523 optimal weight: 5.9990 chunk 510 optimal weight: 30.0000 chunk 389 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 191 optimal weight: 50.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 112 HIS ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 13 ASN ** W 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.066851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.042361 restraints weight = 373927.617| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.52 r_work: 0.2764 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 88826 Z= 0.239 Angle : 0.668 11.020 133297 Z= 0.337 Chirality : 0.038 0.438 17141 Planarity : 0.005 0.067 6884 Dihedral : 25.433 179.645 45199 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.30 % Allowed : 22.25 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -1.00 (0.15), residues: 3026 helix: 0.57 (0.18), residues: 896 sheet: -0.38 (0.22), residues: 537 loop : -1.52 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP W 296 HIS 0.008 0.001 HIS F 39 PHE 0.012 0.001 PHE Y 94 TYR 0.014 0.001 TYR Q 54 ARG 0.003 0.000 ARG O 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 253 time to evaluate : 3.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.8959 (mm110) cc_final: 0.8673 (mm110) REVERT: C 198 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8971 (pt0) REVERT: F 10 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6619 (mm-30) REVERT: F 59 GLN cc_start: 0.8363 (tp40) cc_final: 0.7381 (mp10) REVERT: G 61 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8118 (pm20) REVERT: G 72 ASP cc_start: 0.8769 (m-30) cc_final: 0.8422 (m-30) REVERT: G 118 GLN cc_start: 0.9474 (OUTLIER) cc_final: 0.9189 (tm-30) REVERT: H 37 ASP cc_start: 0.8714 (m-30) cc_final: 0.8485 (m-30) REVERT: H 47 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7516 (t) REVERT: I 90 GLU cc_start: 0.8940 (tp30) cc_final: 0.8635 (tp30) REVERT: I 95 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6736 (tm) REVERT: J 102 MET cc_start: 0.9026 (mtp) cc_final: 0.8628 (mtp) REVERT: M 28 GLU cc_start: 0.8769 (tm-30) cc_final: 0.7898 (tm-30) REVERT: M 31 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8448 (pm20) REVERT: M 36 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: P 31 ASP cc_start: 0.9010 (t70) cc_final: 0.8528 (t0) REVERT: Q 76 LYS cc_start: 0.5968 (mmmm) cc_final: 0.5653 (ttpp) REVERT: R 30 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8629 (t80) REVERT: S 5 GLU cc_start: 0.8597 (mp0) cc_final: 0.7397 (mp0) REVERT: T 16 ARG cc_start: 0.9544 (OUTLIER) cc_final: 0.8625 (ttp80) REVERT: T 27 MET cc_start: 0.8620 (mmm) cc_final: 0.8317 (tpp) REVERT: V 165 LYS cc_start: 0.8873 (tppt) cc_final: 0.8621 (tptp) REVERT: W 318 GLN cc_start: 0.9157 (mt0) cc_final: 0.8508 (tt0) REVERT: W 326 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8657 (mm) outliers start: 83 outliers final: 64 residues processed: 328 average time/residue: 0.6238 time to fit residues: 356.3269 Evaluate side-chains 318 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 243 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 98 GLU 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 P residue 33 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 4 ASN Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain S residue 37 HIS Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 16 ARG 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 22 LYS Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 136 LEU Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 372 THR Chi-restraints excluded: chain W residue 424 GLU Chi-restraints excluded: chain Y residue 131 LEU Chi-restraints excluded: chain Y residue 196 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 143 optimal weight: 30.0000 chunk 380 optimal weight: 40.0000 chunk 361 optimal weight: 5.9990 chunk 374 optimal weight: 8.9990 chunk 287 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 356 optimal weight: 5.9990 chunk 496 optimal weight: 20.0000 chunk 543 optimal weight: 2.9990 chunk 303 optimal weight: 7.9990 chunk 214 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 ASN V 69 GLN ** W 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.066548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.041975 restraints weight = 373454.995| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.55 r_work: 0.2749 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 88826 Z= 0.284 Angle : 0.681 9.799 133297 Z= 0.344 Chirality : 0.039 0.437 17141 Planarity : 0.005 0.069 6884 Dihedral : 25.398 179.775 45199 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 3.38 % Allowed : 22.37 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 3026 helix: 0.62 (0.18), residues: 891 sheet: -0.36 (0.22), residues: 537 loop : -1.50 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 296 HIS 0.006 0.001 HIS F 112 PHE 0.015 0.001 PHE C 257 TYR 0.020 0.001 TYR F 110 ARG 0.005 0.000 ARG F 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 250 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.8966 (mm110) cc_final: 0.8683 (mm110) REVERT: F 10 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6655 (mm-30) REVERT: F 59 GLN cc_start: 0.8393 (tp40) cc_final: 0.7400 (mp10) REVERT: G 61 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8144 (pm20) REVERT: G 72 ASP cc_start: 0.8784 (m-30) cc_final: 0.8439 (m-30) REVERT: G 118 GLN cc_start: 0.9485 (OUTLIER) cc_final: 0.9200 (tm-30) REVERT: I 95 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6666 (tm) REVERT: J 102 MET cc_start: 0.9035 (mtp) cc_final: 0.8650 (mtp) REVERT: M 28 GLU cc_start: 0.8755 (tm-30) cc_final: 0.7870 (tm-30) REVERT: M 31 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8442 (pm20) REVERT: M 36 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7796 (mm-30) REVERT: P 31 ASP cc_start: 0.9006 (t70) cc_final: 0.8535 (t0) REVERT: Q 76 LYS cc_start: 0.6227 (mmmm) cc_final: 0.5741 (ttpp) REVERT: R 30 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8660 (t80) REVERT: S 5 GLU cc_start: 0.8583 (mp0) cc_final: 0.7402 (mp0) REVERT: T 16 ARG cc_start: 0.9575 (OUTLIER) cc_final: 0.8624 (ttp80) REVERT: T 27 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8376 (tpp) REVERT: V 165 LYS cc_start: 0.8858 (tppt) cc_final: 0.8584 (tptp) REVERT: W 318 GLN cc_start: 0.9179 (mt0) cc_final: 0.8548 (tt0) REVERT: W 326 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8670 (mm) REVERT: Y 109 PHE cc_start: 0.7628 (m-10) cc_final: 0.7333 (t80) outliers start: 85 outliers final: 67 residues processed: 325 average time/residue: 0.6201 time to fit residues: 352.4867 Evaluate side-chains 324 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 247 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 4 ASN Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 22 LYS Chi-restraints excluded: chain V residue 111 MET Chi-restraints excluded: chain V residue 136 LEU Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 372 THR Chi-restraints excluded: chain W residue 424 GLU Chi-restraints excluded: chain Y residue 131 LEU Chi-restraints excluded: chain Y residue 196 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 297 optimal weight: 5.9990 chunk 508 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 368 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 347 optimal weight: 8.9990 chunk 384 optimal weight: 30.0000 chunk 533 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 266 optimal weight: 50.0000 chunk 9 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 69 GLN ** W 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.065887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.041264 restraints weight = 375883.097| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.61 r_work: 0.2719 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 88826 Z= 0.384 Angle : 0.739 10.989 133297 Z= 0.372 Chirality : 0.042 0.445 17141 Planarity : 0.005 0.072 6884 Dihedral : 25.438 179.908 45199 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.11 % Favored : 93.85 % Rotamer: Outliers : 3.26 % Allowed : 22.33 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -1.10 (0.15), residues: 3026 helix: 0.48 (0.18), residues: 894 sheet: -0.44 (0.22), residues: 535 loop : -1.57 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 296 HIS 0.006 0.001 HIS L 29 PHE 0.012 0.001 PHE Y 94 TYR 0.020 0.002 TYR F 110 ARG 0.005 0.000 ARG F 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6052 Ramachandran restraints generated. 3026 Oldfield, 0 Emsley, 3026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 247 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.8975 (mm110) cc_final: 0.8696 (mm110) REVERT: E 72 ARG cc_start: 0.5371 (mtm180) cc_final: 0.5007 (mtm180) REVERT: F 10 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6605 (mm-30) REVERT: F 59 GLN cc_start: 0.8393 (tp40) cc_final: 0.7395 (mp10) REVERT: G 61 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8144 (pm20) REVERT: G 72 ASP cc_start: 0.8862 (m-30) cc_final: 0.8520 (m-30) REVERT: G 118 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.9223 (tm-30) REVERT: H 37 ASP cc_start: 0.8763 (m-30) cc_final: 0.8500 (m-30) REVERT: H 47 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7568 (t) REVERT: I 95 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6450 (tm) REVERT: J 102 MET cc_start: 0.9062 (mtp) cc_final: 0.8652 (mtp) REVERT: M 28 GLU cc_start: 0.8745 (tm-30) cc_final: 0.7671 (tm-30) REVERT: M 31 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: M 36 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7805 (mm-30) REVERT: P 31 ASP cc_start: 0.8999 (t70) cc_final: 0.8499 (t0) REVERT: Q 76 LYS cc_start: 0.6242 (mmmm) cc_final: 0.5682 (ttpp) REVERT: R 30 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8640 (t80) REVERT: S 5 GLU cc_start: 0.8607 (mp0) cc_final: 0.7413 (mp0) REVERT: T 16 ARG cc_start: 0.9581 (OUTLIER) cc_final: 0.8615 (ttp80) REVERT: T 27 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8120 (tpp) REVERT: V 165 LYS cc_start: 0.8867 (tppt) cc_final: 0.8588 (tptp) REVERT: W 318 GLN cc_start: 0.9195 (mt0) cc_final: 0.8557 (tt0) REVERT: W 326 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8657 (mm) REVERT: Y 109 PHE cc_start: 0.7618 (m-10) cc_final: 0.7300 (t80) outliers start: 82 outliers final: 65 residues processed: 321 average time/residue: 0.6284 time to fit residues: 349.7073 Evaluate side-chains 321 residues out of total 2593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 245 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain V residue 22 LYS Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 136 LEU Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 45 SER Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 372 THR Chi-restraints excluded: chain W residue 424 GLU Chi-restraints excluded: chain Y residue 196 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 531 optimal weight: 6.9990 chunk 217 optimal weight: 40.0000 chunk 91 optimal weight: 50.0000 chunk 343 optimal weight: 40.0000 chunk 468 optimal weight: 8.9990 chunk 292 optimal weight: 8.9990 chunk 540 optimal weight: 5.9990 chunk 384 optimal weight: 50.0000 chunk 208 optimal weight: 50.0000 chunk 395 optimal weight: 3.9990 chunk 436 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS ** W 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.066386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.041832 restraints weight = 375338.849| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.54 r_work: 0.2744 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 88826 Z= 0.287 Angle : 0.693 11.279 133297 Z= 0.350 Chirality : 0.039 0.436 17141 Planarity : 0.005 0.069 6884 Dihedral : 25.411 179.930 45199 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.10 % Allowed : 22.57 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3026 helix: 0.55 (0.18), residues: 896 sheet: -0.36 (0.22), residues: 535 loop : -1.54 (0.14), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 71 HIS 0.006 0.001 HIS L 29 PHE 0.019 0.001 PHE Y 189 TYR 0.018 0.001 TYR F 110 ARG 0.009 0.000 ARG R 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46179.00 seconds wall clock time: 789 minutes 51.64 seconds (47391.64 seconds total)