Starting phenix.real_space_refine (version: dev) on Fri Dec 16 21:13:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as9_11890/12_2022/7as9_11890.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as9_11890/12_2022/7as9_11890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as9_11890/12_2022/7as9_11890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as9_11890/12_2022/7as9_11890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as9_11890/12_2022/7as9_11890.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as9_11890/12_2022/7as9_11890.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "0 ARG 107": "NH1" <-> "NH2" Residue "0 ARG 116": "NH1" <-> "NH2" Residue "0 ARG 125": "NH1" <-> "NH2" Residue "0 ARG 183": "NH1" <-> "NH2" Residue "0 PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 238": "NH1" <-> "NH2" Residue "0 ARG 265": "NH1" <-> "NH2" Residue "0 ARG 276": "NH1" <-> "NH2" Residue "0 ARG 296": "NH1" <-> "NH2" Residue "0 ARG 302": "NH1" <-> "NH2" Residue "0 TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 395": "NH1" <-> "NH2" Residue "0 ARG 417": "NH1" <-> "NH2" Residue "0 ARG 433": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "E ARG 260": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "G ARG 45": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 168": "NH1" <-> "NH2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "I ARG 3": "NH1" <-> "NH2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I ARG 172": "NH1" <-> "NH2" Residue "K ARG 45": "NH1" <-> "NH2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "K ARG 106": "NH1" <-> "NH2" Residue "L TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N ARG 144": "NH1" <-> "NH2" Residue "O ARG 70": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "R ARG 108": "NH1" <-> "NH2" Residue "S ARG 97": "NH1" <-> "NH2" Residue "S ARG 114": "NH1" <-> "NH2" Residue "T ARG 39": "NH1" <-> "NH2" Residue "T ARG 93": "NH1" <-> "NH2" Residue "T ARG 109": "NH1" <-> "NH2" Residue "U ARG 3": "NH1" <-> "NH2" Residue "U ARG 58": "NH1" <-> "NH2" Residue "V ARG 67": "NH1" <-> "NH2" Residue "V ARG 75": "NH1" <-> "NH2" Residue "V ARG 89": "NH1" <-> "NH2" Residue "W ARG 86": "NH1" <-> "NH2" Residue "Y TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 28": "NH1" <-> "NH2" Residue "a ARG 79": "NH1" <-> "NH2" Residue "b ARG 27": "NH1" <-> "NH2" Residue "b ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 93137 Number of models: 1 Model: "" Number of chains: 32 Chain: "0" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 3987 Classifications: {'peptide': 535} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 508} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "2" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1603 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 30, 'rna3p_pyr': 31} Link IDs: {'rna2p': 13, 'rna3p': 61} Chain: "A" Number of atoms: 60389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2812, 60389 Inner-chain residues flagged as termini: ['pdbres=" G A1220 "'] Classifications: {'RNA': 2812} Modifications used: {'5*END': 2, 'rna2p_pur': 284, 'rna2p_pyr': 145, 'rna3p_pur': 1350, 'rna3p_pyr': 1033} Link IDs: {'rna2p': 429, 'rna3p': 2382} Chain breaks: 5 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 97} Chain: "E" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "F" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "G" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "H" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1284 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "I" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "K" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 974 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 10, 'TRANS': 121} Chain: "L" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 2 Chain: "N" 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: "O" 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: "P" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1081 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "Q" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "R" 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: "S" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "T" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 944 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "U" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "V" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "W" 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: "X" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 725 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "Y" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "a" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "c" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" 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: "f" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 418 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "g" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "h" 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: "i" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "j" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Time building chain proxies: 39.84, per 1000 atoms: 0.43 Number of scatterers: 93137 At special positions: 0 Unit cell: (218.94, 247.64, 221.4, 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 100 16.00 P 2996 15.00 O 26007 8.00 N 17303 7.00 C 46731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS f 30 " - pdb=" SG CYS f 43 " distance=2.03 Simple disulfide: pdb=" SG CYS f 33 " - pdb=" SG CYS f 46 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 49.51 Conformation dependent library (CDL) restraints added in 4.2 seconds 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6820 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 55 sheets defined 31.0% alpha, 17.0% beta 1029 base pairs and 1514 stacking pairs defined. Time for finding SS restraints: 32.64 Creating SS restraints... Processing helix chain '0' and resid 5 through 20 removed outlier: 4.406A pdb=" N LYS 0 18 " --> pdb=" O GLU 0 14 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET 0 20 " --> pdb=" O ASN 0 16 " (cutoff:3.500A) Processing helix chain '0' and resid 73 through 83 Processing helix chain '0' and resid 180 through 185 removed outlier: 4.364A pdb=" N HIS 0 184 " --> pdb=" O ASP 0 180 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 200 removed outlier: 3.734A pdb=" N GLN 0 195 " --> pdb=" O ARG 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 204 through 214 Processing helix chain '0' and resid 223 through 237 Processing helix chain '0' and resid 269 through 274 removed outlier: 3.734A pdb=" N LEU 0 274 " --> pdb=" O LEU 0 270 " (cutoff:3.500A) Processing helix chain '0' and resid 274 through 317 removed outlier: 3.671A pdb=" N GLU 0 283 " --> pdb=" O PHE 0 279 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG 0 284 " --> pdb=" O GLY 0 280 " (cutoff:3.500A) Processing helix chain '0' and resid 322 through 335 removed outlier: 6.515A pdb=" N TYR 0 328 " --> pdb=" O GLU 0 324 " (cutoff:3.500A) Processing helix chain '0' and resid 368 through 414 removed outlier: 3.967A pdb=" N SER 0 413 " --> pdb=" O GLN 0 409 " (cutoff:3.500A) Processing helix chain '0' and resid 415 through 429 Processing helix chain '0' and resid 466 through 474 Processing helix chain '0' and resid 503 through 518 Processing helix chain '0' and resid 532 through 536 Processing helix chain '0' and resid 561 through 565 Processing helix chain 'E' and resid 207 through 215 removed outlier: 4.120A pdb=" N SER E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 225 removed outlier: 3.705A pdb=" N VAL E 224 " --> pdb=" O ARG E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 269 Processing helix chain 'F' and resid 62 through 72 removed outlier: 4.322A pdb=" N ALA F 72 " --> pdb=" O HIS F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 102 through 121 Processing helix chain 'G' and resid 135 through 146 removed outlier: 4.137A pdb=" N MET G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 166 Processing helix chain 'G' and resid 183 through 189 Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'H' and resid 3 through 11 Processing helix chain 'H' and resid 11 through 21 removed outlier: 3.756A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 41 through 46 removed outlier: 3.519A pdb=" N VAL H 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 61 removed outlier: 4.126A pdb=" N ASP H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ALA H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 57 " --> pdb=" O ALA H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 93 through 106 Processing helix chain 'H' and resid 106 through 111 removed outlier: 3.961A pdb=" N VAL H 111 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 59 through 68 removed outlier: 3.727A pdb=" N ALA I 64 " --> pdb=" O LYS I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 153 removed outlier: 3.763A pdb=" N VAL I 152 " --> pdb=" O ASN I 148 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG I 153 " --> pdb=" O ILE I 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 28 removed outlier: 3.973A pdb=" N VAL K 24 " --> pdb=" O PRO K 20 " (cutoff:3.500A) Proline residue: K 26 - end of helix Processing helix chain 'K' and resid 34 through 46 Processing helix chain 'K' and resid 74 through 84 Processing helix chain 'K' and resid 102 through 113 Processing helix chain 'K' and resid 120 through 135 Processing helix chain 'L' and resid 6 through 22 Processing helix chain 'L' and resid 34 through 49 Processing helix chain 'L' and resid 56 through 66 Processing helix chain 'L' and resid 93 through 104 Processing helix chain 'L' and resid 119 through 127 Processing helix chain 'N' and resid 25 through 39 removed outlier: 4.172A pdb=" N GLU N 32 " --> pdb=" O ARG N 28 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA N 35 " --> pdb=" O SER N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 63 removed outlier: 3.917A pdb=" N ILE N 63 " --> pdb=" O ALA N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 73 Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'N' and resid 97 through 110 removed outlier: 3.791A pdb=" N MET N 101 " --> pdb=" O TYR N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 122 removed outlier: 3.727A pdb=" N LYS N 122 " --> pdb=" O GLN N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 137 Processing helix chain 'O' and resid 111 through 118 Processing helix chain 'P' and resid 92 through 100 Processing helix chain 'P' and resid 129 through 140 Processing helix chain 'Q' and resid 43 through 58 Processing helix chain 'Q' and resid 110 through 123 Processing helix chain 'R' and resid 9 through 28 Processing helix chain 'R' and resid 34 through 54 removed outlier: 3.609A pdb=" N GLU R 39 " --> pdb=" O THR R 35 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER R 42 " --> pdb=" O LYS R 38 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL R 43 " --> pdb=" O GLU R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 66 Processing helix chain 'R' and resid 79 through 91 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 70 through 88 Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'T' and resid 2 through 10 Processing helix chain 'T' and resid 53 through 56 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 26 through 31 Processing helix chain 'U' and resid 32 through 72 removed outlier: 3.818A pdb=" N LYS U 41 " --> pdb=" O GLN U 37 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG U 51 " --> pdb=" O PHE U 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS U 54 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG U 55 " --> pdb=" O ARG U 51 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG U 58 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS U 59 " --> pdb=" O ARG U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 87 Processing helix chain 'U' and resid 91 through 101 Processing helix chain 'U' and resid 102 through 117 Processing helix chain 'W' and resid 13 through 23 removed outlier: 3.763A pdb=" N ALA W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 43 through 62 Processing helix chain 'X' and resid 3 through 7 Processing helix chain 'X' and resid 14 through 22 Processing helix chain 'X' and resid 35 through 47 Processing helix chain 'b' and resid 19 through 23 removed outlier: 4.097A pdb=" N ASN b 23 " --> pdb=" O HIS b 20 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 55 Processing helix chain 'c' and resid 2 through 7 Processing helix chain 'c' and resid 12 through 35 Processing helix chain 'c' and resid 40 through 65 removed outlier: 3.973A pdb=" N ARG c 44 " --> pdb=" O THR c 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE c 57 " --> pdb=" O MET c 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 27 Processing helix chain 'd' and resid 40 through 51 Processing helix chain 'f' and resid 9 through 18 Processing helix chain 'h' and resid 8 through 16 Processing helix chain 'h' and resid 24 through 36 removed outlier: 3.661A pdb=" N LEU h 29 " --> pdb=" O LYS h 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL h 30 " --> pdb=" O ASN h 26 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU h 31 " --> pdb=" O GLY h 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 14 Processing helix chain 'i' and resid 18 through 20 No H-bonds generated for 'chain 'i' and resid 18 through 20' Processing helix chain 'i' and resid 37 through 46 removed outlier: 3.973A pdb=" N LYS i 46 " --> pdb=" O ARG i 42 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 59 Processing helix chain 'i' and resid 60 through 63 removed outlier: 4.233A pdb=" N ALA i 63 " --> pdb=" O GLN i 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 60 through 63' Processing sheet with id=AA1, first strand: chain '0' and resid 24 through 28 removed outlier: 6.493A pdb=" N ILE 0 24 " --> pdb=" O ARG 0 40 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ARG 0 40 " --> pdb=" O ILE 0 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 86 through 88 Processing sheet with id=AA3, first strand: chain '0' and resid 92 through 93 Processing sheet with id=AA4, first strand: chain '0' and resid 119 through 120 Processing sheet with id=AA5, first strand: chain '0' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain '0' and resid 242 through 244 Processing sheet with id=AA7, first strand: chain '0' and resid 451 through 454 removed outlier: 4.350A pdb=" N GLU 0 451 " --> pdb=" O VAL 0 463 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE 0 483 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '0' and resid 526 through 530 Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AB2, first strand: chain 'E' and resid 101 through 105 removed outlier: 3.804A pdb=" N ARG E 102 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 91 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL E 81 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU E 93 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 130 through 131 removed outlier: 7.903A pdb=" N ARG E 189 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE E 144 " --> pdb=" O ARG E 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 164 through 167 removed outlier: 5.809A pdb=" N VAL E 164 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG E 175 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 16 removed outlier: 5.921A pdb=" N LYS F 9 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLU F 29 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY F 11 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU F 185 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL F 179 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU F 187 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLU F 175 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL F 108 " --> pdb=" O ASN F 173 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL F 113 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU F 199 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 82 through 83 removed outlier: 3.604A pdb=" N LEU F 83 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE F 49 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN F 50 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 118 through 120 removed outlier: 3.899A pdb=" N GLY F 118 " --> pdb=" O MET F 164 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 3 through 7 removed outlier: 6.240A pdb=" N VAL G 4 " --> pdb=" O ASP G 16 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASP G 16 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU G 6 " --> pdb=" O ALA G 14 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 123 through 125 removed outlier: 6.338A pdb=" N LEU G 153 " --> pdb=" O LEU G 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 31 through 37 removed outlier: 9.922A pdb=" N ILE H 34 " --> pdb=" O THR H 158 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N THR H 158 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE H 36 " --> pdb=" O ILE H 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 66 through 70 removed outlier: 6.462A pdb=" N VAL H 66 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY H 86 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR H 68 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 9 through 10 removed outlier: 3.501A pdb=" N LEU I 9 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 16 through 19 Processing sheet with id=AC5, first strand: chain 'I' and resid 84 through 89 Processing sheet with id=AC6, first strand: chain 'I' and resid 96 through 98 Processing sheet with id=AC7, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.716A pdb=" N SER K 65 " --> pdb=" O TYR K 61 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 99 through 101 Processing sheet with id=AC9, first strand: chain 'L' and resid 51 through 54 removed outlier: 6.944A pdb=" N ASP L 29 " --> pdb=" O ILE L 108 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE L 108 " --> pdb=" O ASP L 29 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 124 through 125 removed outlier: 6.503A pdb=" N VAL N 55 " --> pdb=" O ASN N 124 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TRP N 16 " --> pdb=" O GLU N 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 74 through 78 Processing sheet with id=AD3, first strand: chain 'O' and resid 7 through 10 removed outlier: 6.687A pdb=" N ARG O 17 " --> pdb=" O VAL O 10 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA O 16 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA O 46 " --> pdb=" O ALA O 16 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU O 18 " --> pdb=" O LYS O 44 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL O 40 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL O 24 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL O 38 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA O 83 " --> pdb=" O VAL O 63 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N CYS O 84 " --> pdb=" O ARG O 7 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LYS O 9 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE O 86 " --> pdb=" O LYS O 9 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 76 through 79 removed outlier: 6.751A pdb=" N THR T 58 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG T 50 " --> pdb=" O THR T 58 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR T 60 " --> pdb=" O ILE T 48 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE T 64 " --> pdb=" O GLU T 44 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLU T 44 " --> pdb=" O ILE T 64 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR T 25 " --> pdb=" O VAL T 86 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL T 86 " --> pdb=" O THR T 25 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ARG T 27 " --> pdb=" O ILE T 84 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE T 84 " --> pdb=" O ARG T 27 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS T 29 " --> pdb=" O ALA T 82 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 101 through 102 Processing sheet with id=AD6, first strand: chain 'P' and resid 75 through 77 removed outlier: 5.605A pdb=" N ALA P 75 " --> pdb=" O LYS P 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'Q' and resid 102 through 104 removed outlier: 6.969A pdb=" N ILE Q 34 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 41 through 42 Processing sheet with id=AD9, first strand: chain 'R' and resid 29 through 33 removed outlier: 3.979A pdb=" N MET R 114 " --> pdb=" O LEU R 104 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 70 through 72 removed outlier: 6.309A pdb=" N GLN R 77 " --> pdb=" O ALA R 71 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 30 through 34 removed outlier: 6.495A pdb=" N ALA S 42 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER S 55 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE S 44 " --> pdb=" O LEU S 53 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 11 through 14 removed outlier: 3.866A pdb=" N ILE V 4 " --> pdb=" O LEU V 39 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU V 39 " --> pdb=" O ILE V 4 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 19 through 23 removed outlier: 7.586A pdb=" N VAL V 82 " --> pdb=" O TYR V 76 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR V 76 " --> pdb=" O VAL V 82 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS V 84 " --> pdb=" O PHE V 74 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE V 74 " --> pdb=" O LYS V 84 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN V 86 " --> pdb=" O THR V 72 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR V 72 " --> pdb=" O GLN V 86 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS V 88 " --> pdb=" O LYS V 70 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS V 70 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN V 90 " --> pdb=" O ALA V 68 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS V 64 " --> pdb=" O LYS V 94 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR V 96 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL V 62 " --> pdb=" O THR V 96 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU V 98 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA V 60 " --> pdb=" O GLU V 98 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 3 through 11 removed outlier: 5.949A pdb=" N SER W 101 " --> pdb=" O THR W 9 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG W 11 " --> pdb=" O ARG W 99 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ARG W 99 " --> pdb=" O ARG W 11 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE W 96 " --> pdb=" O LEU W 82 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU W 82 " --> pdb=" O ILE W 96 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS W 98 " --> pdb=" O PRO W 80 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR W 100 " --> pdb=" O GLU W 78 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU W 78 " --> pdb=" O THR W 100 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS W 102 " --> pdb=" O VAL W 76 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL W 76 " --> pdb=" O HIS W 102 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR W 104 " --> pdb=" O ALA W 74 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA W 74 " --> pdb=" O THR W 104 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL W 106 " --> pdb=" O SER W 72 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 8 through 11 removed outlier: 3.542A pdb=" N LYS X 9 " --> pdb=" O GLU X 29 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU X 29 " --> pdb=" O LYS X 9 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR X 27 " --> pdb=" O PRO X 11 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG X 77 " --> pdb=" O VAL X 30 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 9 through 11 Processing sheet with id=AE8, first strand: chain 'Y' and resid 23 through 27 removed outlier: 3.986A pdb=" N ALA Y 25 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 40 through 43 Processing sheet with id=AF1, first strand: chain 'Y' and resid 81 through 85 Processing sheet with id=AF2, first strand: chain 'a' and resid 30 through 31 removed outlier: 5.683A pdb=" N ILE a 44 " --> pdb=" O ALA a 69 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA a 69 " --> pdb=" O ILE a 44 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 38 through 39 removed outlier: 3.782A pdb=" N TYR a 54 " --> pdb=" O LYS a 85 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL a 87 " --> pdb=" O TYR a 54 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'b' and resid 34 through 36 Processing sheet with id=AF5, first strand: chain 'd' and resid 35 through 38 Processing sheet with id=AF6, first strand: chain 'f' and resid 27 through 29 Processing sheet with id=AF7, first strand: chain 'f' and resid 48 through 49 Processing sheet with id=AF8, first strand: chain 'g' and resid 18 through 22 Processing sheet with id=AF9, first strand: chain 'i' and resid 15 through 16 removed outlier: 3.729A pdb=" N LYS i 15 " --> pdb=" O LYS i 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'j' and resid 15 through 19 1079 hydrogen bonds defined for protein. 3015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2618 hydrogen bonds 4240 hydrogen bond angles 0 basepair planarities 1029 basepair parallelities 1514 stacking parallelities Total time for adding SS restraints: 153.71 Time building geometry restraints manager: 52.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 13902 1.33 - 1.45: 42374 1.45 - 1.57: 38787 1.57 - 1.70: 5989 1.70 - 1.82: 184 Bond restraints: 101236 Sorted by residual: bond pdb=" C VAL H 155 " pdb=" N ILE H 156 " ideal model delta sigma weight residual 1.333 1.460 -0.127 1.20e-02 6.94e+03 1.13e+02 bond pdb=" CA VAL H 35 " pdb=" CB VAL H 35 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.36e-02 5.41e+03 1.96e+01 bond pdb=" N VAL H 155 " pdb=" CA VAL H 155 " ideal model delta sigma weight residual 1.459 1.514 -0.055 1.25e-02 6.40e+03 1.92e+01 bond pdb=" C TYR V 76 " pdb=" N LYS V 77 " ideal model delta sigma weight residual 1.330 1.271 0.059 1.47e-02 4.63e+03 1.62e+01 bond pdb=" CA ASP U 102 " pdb=" CB ASP U 102 " ideal model delta sigma weight residual 1.523 1.475 0.049 1.27e-02 6.20e+03 1.46e+01 ... (remaining 101231 not shown) Histogram of bond angle deviations from ideal: 94.28 - 107.00: 19852 107.00 - 119.71: 89267 119.71 - 132.43: 42153 132.43 - 145.15: 250 145.15 - 157.86: 1 Bond angle restraints: 151523 Sorted by residual: angle pdb=" CA LEU I 72 " pdb=" CB LEU I 72 " pdb=" CG LEU I 72 " ideal model delta sigma weight residual 116.30 157.86 -41.56 3.50e+00 8.16e-02 1.41e+02 angle pdb=" N VAL I 80 " pdb=" CA VAL I 80 " pdb=" CB VAL I 80 " ideal model delta sigma weight residual 110.62 119.28 -8.66 1.05e+00 9.07e-01 6.81e+01 angle pdb=" N THR I 69 " pdb=" CA THR I 69 " pdb=" C THR I 69 " ideal model delta sigma weight residual 112.93 122.06 -9.13 1.12e+00 7.97e-01 6.65e+01 angle pdb=" N PRO 0 544 " pdb=" CA PRO 0 544 " pdb=" CB PRO 0 544 " ideal model delta sigma weight residual 103.25 111.56 -8.31 1.05e+00 9.07e-01 6.27e+01 angle pdb=" N PRO 0 491 " pdb=" CA PRO 0 491 " pdb=" CB PRO 0 491 " ideal model delta sigma weight residual 103.25 111.03 -7.78 1.05e+00 9.07e-01 5.49e+01 ... (remaining 151518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 51441 35.98 - 71.97: 2362 71.97 - 107.95: 244 107.95 - 143.94: 38 143.94 - 179.92: 42 Dihedral angle restraints: 54127 sinusoidal: 43540 harmonic: 10587 Sorted by residual: dihedral pdb=" CB CYS f 33 " pdb=" SG CYS f 33 " pdb=" SG CYS f 46 " pdb=" CB CYS f 46 " ideal model delta sinusoidal sigma weight residual -86.00 -175.78 89.78 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CA ASN V 50 " pdb=" C ASN V 50 " pdb=" N PRO V 51 " pdb=" CA PRO V 51 " ideal model delta harmonic sigma weight residual 180.00 132.84 47.16 0 5.00e+00 4.00e-02 8.90e+01 dihedral pdb=" CA VAL 0 203 " pdb=" C VAL 0 203 " pdb=" N SER 0 204 " pdb=" CA SER 0 204 " ideal model delta harmonic sigma weight residual 180.00 133.10 46.90 0 5.00e+00 4.00e-02 8.80e+01 ... (remaining 54124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 18183 0.088 - 0.175: 1123 0.175 - 0.263: 72 0.263 - 0.350: 8 0.350 - 0.438: 3 Chirality restraints: 19389 Sorted by residual: chirality pdb=" C1' G A1757 " pdb=" O4' G A1757 " pdb=" C2' G A1757 " pdb=" N9 G A1757 " both_signs ideal model delta sigma weight residual False 2.46 2.02 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CA VAL H 35 " pdb=" N VAL H 35 " pdb=" C VAL H 35 " pdb=" CB VAL H 35 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" C3' G A1828 " pdb=" C4' G A1828 " pdb=" O3' G A1828 " pdb=" C2' G A1828 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 19386 not shown) Planarity restraints: 8035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 68 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C THR I 68 " -0.077 2.00e-02 2.50e+03 pdb=" O THR I 68 " 0.029 2.00e-02 2.50e+03 pdb=" N THR I 69 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 9 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.68e+01 pdb=" C ASN H 9 " 0.071 2.00e-02 2.50e+03 pdb=" O ASN H 9 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS H 10 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1304 " 0.047 2.00e-02 2.50e+03 2.05e-02 1.26e+01 pdb=" N9 G A1304 " -0.048 2.00e-02 2.50e+03 pdb=" C8 G A1304 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A1304 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G A1304 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A1304 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A1304 " 0.016 2.00e-02 2.50e+03 pdb=" N1 G A1304 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A1304 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G A1304 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A1304 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G A1304 " -0.007 2.00e-02 2.50e+03 ... (remaining 8032 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 1528 2.56 - 3.15: 79508 3.15 - 3.73: 207099 3.73 - 4.32: 259190 4.32 - 4.90: 351402 Nonbonded interactions: 898727 Sorted by model distance: nonbonded pdb=" O2 C A2841 " pdb=" O2' A A2908 " model vdw 1.976 2.440 nonbonded pdb=" O4 U A1058 " pdb=" OG SER N 31 " model vdw 1.995 2.440 nonbonded pdb=" O LYS R 46 " pdb=" OG1 THR R 49 " model vdw 2.001 2.440 nonbonded pdb=" O ALA G 109 " pdb=" OG SER G 112 " model vdw 2.005 2.440 nonbonded pdb=" O2 U A1081 " pdb=" O6 G A1166 " model vdw 2.009 2.432 ... (remaining 898722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2996 5.49 5 S 100 5.16 5 C 46731 2.51 5 N 17303 2.21 5 O 26007 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 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: 0.050 Extract box with map and model: 20.560 Check model and map are aligned: 1.040 Convert atoms to be neutral: 0.610 Process input model: 344.730 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 374.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 : 0.007 0.127 101236 Z= 0.430 Angle : 0.982 41.562 151523 Z= 0.510 Chirality : 0.048 0.438 19389 Planarity : 0.007 0.086 8035 Dihedral : 17.120 179.922 47301 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.03 % Favored : 86.62 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.76 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.11), residues: 3646 helix: -2.86 (0.12), residues: 1018 sheet: -3.43 (0.17), residues: 562 loop : -3.47 (0.11), residues: 2066 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1228 time to evaluate : 4.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1230 average time/residue: 0.9648 time to fit residues: 1923.0897 Evaluate side-chains 735 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 735 time to evaluate : 4.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 555 optimal weight: 0.3980 chunk 498 optimal weight: 10.0000 chunk 276 optimal weight: 20.0000 chunk 170 optimal weight: 50.0000 chunk 336 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 515 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 383 optimal weight: 5.9990 chunk 597 optimal weight: 5.9990 overall best weight: 5.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 290 GLN ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN G 40 GLN I 102 ASN I 107 ASN I 129 GLN L 44 GLN L 49 ASN L 103 HIS N 8 ASN N 81 HIS O 109 ASN P 59 GLN Q 123 HIS R 57 HIS R 61 GLN ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 GLN ** W 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 59 GLN ** Y 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 34 GLN ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 ASN ** i 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.110 101236 Z= 0.255 Angle : 0.794 20.260 151523 Z= 0.403 Chirality : 0.041 0.486 19389 Planarity : 0.006 0.079 8035 Dihedral : 17.657 179.884 40020 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.85 % Favored : 90.07 % Rotamer Outliers : 3.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.12), residues: 3646 helix: -1.56 (0.14), residues: 1034 sheet: -2.81 (0.18), residues: 600 loop : -2.89 (0.12), residues: 2012 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 908 time to evaluate : 5.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 60 residues processed: 955 average time/residue: 0.9513 time to fit residues: 1512.0162 Evaluate side-chains 784 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 724 time to evaluate : 4.452 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.7351 time to fit residues: 87.2043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 332 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 497 optimal weight: 20.0000 chunk 406 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 598 optimal weight: 3.9990 chunk 646 optimal weight: 10.0000 chunk 533 optimal weight: 10.0000 chunk 593 optimal weight: 5.9990 chunk 204 optimal weight: 30.0000 chunk 480 optimal weight: 9.9990 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 247 ASN ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN F 184 ASN G 40 GLN G 75 GLN G 182 ASN ** H 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN I 107 ASN N 59 ASN ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN Q 28 HIS S 37 ASN ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 101 ASN W 2 GLN W 95 GLN ** Y 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 101236 Z= 0.305 Angle : 0.794 14.813 151523 Z= 0.405 Chirality : 0.041 0.474 19389 Planarity : 0.006 0.069 8035 Dihedral : 17.711 179.844 40020 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 28.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.61 % Favored : 89.28 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.12), residues: 3646 helix: -1.29 (0.14), residues: 1049 sheet: -2.48 (0.19), residues: 604 loop : -2.69 (0.13), residues: 1993 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 805 time to evaluate : 4.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 60 residues processed: 864 average time/residue: 0.9445 time to fit residues: 1368.7182 Evaluate side-chains 758 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 698 time to evaluate : 4.345 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.7357 time to fit residues: 86.0471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 591 optimal weight: 5.9990 chunk 450 optimal weight: 40.0000 chunk 310 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 285 optimal weight: 20.0000 chunk 401 optimal weight: 0.9980 chunk 600 optimal weight: 9.9990 chunk 636 optimal weight: 0.3980 chunk 313 optimal weight: 20.0000 chunk 569 optimal weight: 5.9990 chunk 171 optimal weight: 50.0000 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN ** F 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** H 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 GLN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 HIS ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 GLN ** Y 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 ASN ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 101236 Z= 0.220 Angle : 0.726 18.941 151523 Z= 0.370 Chirality : 0.038 0.463 19389 Planarity : 0.005 0.067 8035 Dihedral : 17.526 179.271 40020 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.85 % Favored : 90.10 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.13), residues: 3646 helix: -1.05 (0.14), residues: 1046 sheet: -2.24 (0.19), residues: 609 loop : -2.47 (0.13), residues: 1991 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 798 time to evaluate : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 49 residues processed: 834 average time/residue: 0.9138 time to fit residues: 1274.4144 Evaluate side-chains 750 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 701 time to evaluate : 4.355 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.7245 time to fit residues: 70.1293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 529 optimal weight: 8.9990 chunk 361 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 473 optimal weight: 30.0000 chunk 262 optimal weight: 20.0000 chunk 542 optimal weight: 2.9990 chunk 439 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 324 optimal weight: 20.0000 chunk 570 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 HIS ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 290 GLN ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 ASN I 107 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN P 38 GLN R 76 ASN V 86 GLN W 67 ASN Y 59 GLN ** Y 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 101236 Z= 0.273 Angle : 0.752 17.917 151523 Z= 0.383 Chirality : 0.039 0.462 19389 Planarity : 0.006 0.164 8035 Dihedral : 17.617 179.639 40020 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.94 % Favored : 89.00 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.13), residues: 3646 helix: -0.97 (0.14), residues: 1045 sheet: -2.09 (0.19), residues: 595 loop : -2.40 (0.13), residues: 2006 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 761 time to evaluate : 4.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 48 residues processed: 814 average time/residue: 0.8984 time to fit residues: 1228.9550 Evaluate side-chains 745 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 697 time to evaluate : 4.453 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.6983 time to fit residues: 66.8525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 213 optimal weight: 30.0000 chunk 572 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 373 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 636 optimal weight: 20.0000 chunk 528 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 334 optimal weight: 20.0000 overall best weight: 13.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 160 GLN ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 305 ASN ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 HIS ** F 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 GLN ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 GLN P 126 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN U 118 ASN ** V 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 36 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.112 101236 Z= 0.456 Angle : 0.936 13.600 151523 Z= 0.472 Chirality : 0.047 0.441 19389 Planarity : 0.007 0.117 8035 Dihedral : 18.352 179.866 40020 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 44.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.40 % Favored : 87.47 % Rotamer Outliers : 4.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.12), residues: 3646 helix: -1.45 (0.14), residues: 1052 sheet: -2.30 (0.19), residues: 610 loop : -2.68 (0.12), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 730 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 90 residues processed: 807 average time/residue: 0.9222 time to fit residues: 1251.1841 Evaluate side-chains 764 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 674 time to evaluate : 4.348 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 0.7342 time to fit residues: 125.4948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 613 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 chunk 464 optimal weight: 50.0000 chunk 360 optimal weight: 7.9990 chunk 535 optimal weight: 8.9990 chunk 355 optimal weight: 6.9990 chunk 634 optimal weight: 5.9990 chunk 396 optimal weight: 10.0000 chunk 386 optimal weight: 9.9990 chunk 292 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN ** F 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 ASN I 107 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 57 HIS ** U 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 39 ASN ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 101236 Z= 0.278 Angle : 0.781 19.178 151523 Z= 0.398 Chirality : 0.041 0.444 19389 Planarity : 0.006 0.170 8035 Dihedral : 18.045 179.714 40020 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 32.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.14 % Favored : 88.78 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.13), residues: 3646 helix: -1.14 (0.14), residues: 1059 sheet: -2.08 (0.19), residues: 614 loop : -2.58 (0.13), residues: 1973 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 732 time to evaluate : 4.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 36 residues processed: 771 average time/residue: 0.9074 time to fit residues: 1181.2370 Evaluate side-chains 710 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 674 time to evaluate : 4.351 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.6975 time to fit residues: 51.3421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 392 optimal weight: 8.9990 chunk 253 optimal weight: 20.0000 chunk 378 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 403 optimal weight: 3.9990 chunk 432 optimal weight: 20.0000 chunk 313 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 498 optimal weight: 6.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN E 226 ASN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 ASN I 107 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 ASN P 126 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 101236 Z= 0.280 Angle : 0.776 19.854 151523 Z= 0.395 Chirality : 0.041 0.507 19389 Planarity : 0.006 0.128 8035 Dihedral : 17.970 179.730 40020 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 32.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.77 % Favored : 88.12 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.13), residues: 3646 helix: -0.97 (0.15), residues: 1042 sheet: -2.10 (0.19), residues: 613 loop : -2.55 (0.13), residues: 1991 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 734 time to evaluate : 4.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 41 residues processed: 758 average time/residue: 0.9434 time to fit residues: 1198.8300 Evaluate side-chains 717 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 676 time to evaluate : 4.407 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.7583 time to fit residues: 62.0014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 576 optimal weight: 30.0000 chunk 607 optimal weight: 7.9990 chunk 554 optimal weight: 20.0000 chunk 590 optimal weight: 30.0000 chunk 355 optimal weight: 4.9990 chunk 257 optimal weight: 20.0000 chunk 464 optimal weight: 30.0000 chunk 181 optimal weight: 20.0000 chunk 534 optimal weight: 20.0000 chunk 558 optimal weight: 5.9990 chunk 588 optimal weight: 5.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 ASN I 107 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 101236 Z= 0.328 Angle : 0.818 17.605 151523 Z= 0.414 Chirality : 0.042 0.393 19389 Planarity : 0.006 0.212 8035 Dihedral : 18.124 179.865 40020 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 36.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.23 % Favored : 87.63 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.13), residues: 3646 helix: -1.07 (0.15), residues: 1040 sheet: -2.11 (0.19), residues: 634 loop : -2.57 (0.13), residues: 1972 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 696 time to evaluate : 4.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 28 residues processed: 719 average time/residue: 0.9999 time to fit residues: 1224.9406 Evaluate side-chains 688 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 660 time to evaluate : 4.428 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.7801 time to fit residues: 44.7582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 388 optimal weight: 0.6980 chunk 624 optimal weight: 0.2980 chunk 381 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 434 optimal weight: 6.9990 chunk 655 optimal weight: 2.9990 chunk 603 optimal weight: 20.0000 chunk 522 optimal weight: 6.9990 chunk 54 optimal weight: 40.0000 chunk 403 optimal weight: 20.0000 chunk 320 optimal weight: 20.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 300 ASN ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 61 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN ** G 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 ASN ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 GLN ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 59 GLN ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 34 GLN ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 101236 Z= 0.202 Angle : 0.738 20.898 151523 Z= 0.374 Chirality : 0.038 0.484 19389 Planarity : 0.005 0.062 8035 Dihedral : 17.751 179.475 40020 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 26.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.09 % Favored : 89.82 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.13), residues: 3646 helix: -0.95 (0.15), residues: 1058 sheet: -1.82 (0.19), residues: 634 loop : -2.43 (0.13), residues: 1954 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 733 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 741 average time/residue: 0.9002 time to fit residues: 1127.5671 Evaluate side-chains 681 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 669 time to evaluate : 4.364 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.7202 time to fit residues: 20.5181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 414 optimal weight: 6.9990 chunk 556 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 481 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 522 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 536 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 300 ASN ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN O 109 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.041162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.033454 restraints weight = 836240.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.034625 restraints weight = 286364.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.035311 restraints weight = 146039.714| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 101236 Z= 0.351 Angle : 0.837 18.586 151523 Z= 0.422 Chirality : 0.043 0.526 19389 Planarity : 0.006 0.147 8035 Dihedral : 18.103 179.959 40020 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 38.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.34 % Favored : 87.55 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.13), residues: 3646 helix: -1.02 (0.15), residues: 1038 sheet: -1.92 (0.19), residues: 634 loop : -2.48 (0.13), residues: 1974 =============================================================================== Job complete usr+sys time: 19713.04 seconds wall clock time: 351 minutes 21.67 seconds (21081.67 seconds total)