Starting phenix.real_space_refine on Sat Dec 16 06:28:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/12_2023/5ady_3133_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/12_2023/5ady_3133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/12_2023/5ady_3133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/12_2023/5ady_3133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/12_2023/5ady_3133_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/12_2023/5ady_3133_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.040 sd= 0.416 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3021 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 49296 2.51 5 N 18113 2.21 5 O 26831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 97364 Number of models: 1 Model: "" Number of chains: 35 Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1733 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Chain: "6" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3403 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "7" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1231 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2504 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 10, 'rna3p': 106} Chain: "B" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 263, 'rna2p_pyr': 138, 'rna3p_pur': 1411, 'rna3p_pyr': 1091} Link IDs: {'rna2p': 401, 'rna3p': 2501} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1420 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 596 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 38.13, per 1000 atoms: 0.39 Number of scatterers: 97364 At special positions: 0 Unit cell: (232.014, 201.701, 239.009, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 3021 15.00 Mg 1 11.99 O 26831 8.00 N 18113 7.00 C 49296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 57.87 Conformation dependent library (CDL) restraints added in 5.0 seconds 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7678 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 115 helices and 40 sheets defined 24.4% alpha, 8.3% beta 797 base pairs and 999 stacking pairs defined. Time for finding SS restraints: 46.14 Creating SS restraints... Processing helix chain '0' and resid 9 through 15 removed outlier: 4.094A pdb=" N ARG 0 15 " --> pdb=" O LYS 0 11 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 16 removed outlier: 3.976A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 37 Processing helix chain '3' and resid 7 through 10 No H-bonds generated for 'chain '3' and resid 7 through 10' Processing helix chain '3' and resid 37 through 44 removed outlier: 3.638A pdb=" N LEU 3 43 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG 3 44 " --> pdb=" O LYS 3 40 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 60 Processing helix chain '4' and resid 31 through 33 No H-bonds generated for 'chain '4' and resid 31 through 33' Processing helix chain '5' and resid 7 through 11 Processing helix chain '5' and resid 23 through 28 Processing helix chain '5' and resid 82 through 84 No H-bonds generated for 'chain '5' and resid 82 through 84' Processing helix chain '5' and resid 86 through 90 Processing helix chain '5' and resid 151 through 156 Processing helix chain '5' and resid 182 through 197 Processing helix chain '6' and resid 28 through 37 Processing helix chain '6' and resid 60 through 73 Processing helix chain '6' and resid 86 through 95 removed outlier: 3.651A pdb=" N LEU 6 95 " --> pdb=" O ASN 6 91 " (cutoff:3.500A) Processing helix chain '6' and resid 103 through 113 Processing helix chain '6' and resid 118 through 145 removed outlier: 3.850A pdb=" N THR 6 134 " --> pdb=" O ARG 6 130 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG 6 135 " --> pdb=" O HIS 6 131 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL 6 137 " --> pdb=" O ALA 6 133 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG 6 138 " --> pdb=" O THR 6 134 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY 6 139 " --> pdb=" O ARG 6 135 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP 6 140 " --> pdb=" O LEU 6 136 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR 6 141 " --> pdb=" O VAL 6 137 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS 6 142 " --> pdb=" O ARG 6 138 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU 6 143 " --> pdb=" O GLY 6 139 " (cutoff:3.500A) Processing helix chain '6' and resid 161 through 192 removed outlier: 4.044A pdb=" N ARG 6 180 " --> pdb=" O SER 6 176 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL 6 181 " --> pdb=" O ARG 6 177 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER 6 191 " --> pdb=" O GLN 6 187 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG 6 192 " --> pdb=" O GLY 6 188 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 218 Processing helix chain '6' and resid 261 through 267 Processing helix chain '6' and resid 270 through 276 removed outlier: 3.922A pdb=" N GLU 6 273 " --> pdb=" O THR 6 270 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG 6 275 " --> pdb=" O GLN 6 272 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN 6 276 " --> pdb=" O GLU 6 273 " (cutoff:3.500A) Processing helix chain '6' and resid 291 through 304 removed outlier: 3.754A pdb=" N VAL 6 301 " --> pdb=" O ALA 6 297 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU 6 304 " --> pdb=" O THR 6 300 " (cutoff:3.500A) Processing helix chain '6' and resid 350 through 360 Processing helix chain '6' and resid 377 through 386 Processing helix chain '6' and resid 396 through 398 No H-bonds generated for 'chain '6' and resid 396 through 398' Processing helix chain '6' and resid 408 through 417 Processing helix chain '7' and resid 4 through 20 Processing helix chain '7' and resid 34 through 43 Processing helix chain '7' and resid 63 through 66 Processing helix chain '7' and resid 98 through 101 No H-bonds generated for 'chain '7' and resid 98 through 101' Processing helix chain '7' and resid 127 through 131 Processing helix chain '7' and resid 136 through 139 No H-bonds generated for 'chain '7' and resid 136 through 139' Processing helix chain '7' and resid 150 through 153 No H-bonds generated for 'chain '7' and resid 150 through 153' Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 98 through 101 Processing helix chain 'E' and resid 16 through 19 No H-bonds generated for 'chain 'E' and resid 16 through 19' Processing helix chain 'E' and resid 25 through 39 removed outlier: 4.078A pdb=" N VAL E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 115 removed outlier: 3.509A pdb=" N LYS E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 141 removed outlier: 3.969A pdb=" N ASP E 140 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 162 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 190 through 198 removed outlier: 3.792A pdb=" N GLU E 197 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 8 Processing helix chain 'F' and resid 47 through 55 removed outlier: 3.779A pdb=" N ALA F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 59 No H-bonds generated for 'chain 'F' and resid 57 through 59' Processing helix chain 'F' and resid 92 through 106 removed outlier: 4.078A pdb=" N MET F 95 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE F 98 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU F 102 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA F 106 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 168 removed outlier: 3.773A pdb=" N ALA F 167 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU F 168 " --> pdb=" O GLY F 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 5 No H-bonds generated for 'chain 'G' and resid 2 through 5' Processing helix chain 'G' and resid 60 through 79 Processing helix chain 'G' and resid 137 through 151 removed outlier: 4.156A pdb=" N GLY G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 25 No H-bonds generated for 'chain 'H' and resid 23 through 25' Processing helix chain 'H' and resid 44 through 54 removed outlier: 4.405A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 61 Processing helix chain 'H' and resid 71 through 74 No H-bonds generated for 'chain 'H' and resid 71 through 74' Processing helix chain 'I' and resid 20 through 23 No H-bonds generated for 'chain 'I' and resid 20 through 23' Processing helix chain 'I' and resid 27 through 29 No H-bonds generated for 'chain 'I' and resid 27 through 29' Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 75 through 80 Processing helix chain 'I' and resid 102 through 115 removed outlier: 5.683A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 129 through 135 removed outlier: 4.203A pdb=" N SER I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 10 No H-bonds generated for 'chain 'J' and resid 8 through 10' Processing helix chain 'J' and resid 25 through 36 removed outlier: 3.561A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 97 through 108 removed outlier: 3.565A pdb=" N ILE J 103 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA J 104 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY J 107 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 4.377A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'K' and resid 109 through 117 removed outlier: 3.656A pdb=" N ILE K 115 " --> pdb=" O MET K 112 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER K 116 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 5 No H-bonds generated for 'chain 'L' and resid 3 through 5' Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 79 through 84 removed outlier: 3.545A pdb=" N LEU L 82 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.641A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 137 Processing helix chain 'M' and resid 43 through 57 removed outlier: 4.274A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA M 48 " --> pdb=" O ARG M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.528A pdb=" N ARG M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 31 removed outlier: 3.820A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 55 removed outlier: 5.418A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 61 through 66 Processing helix chain 'N' and resid 73 through 78 Processing helix chain 'N' and resid 85 through 87 No H-bonds generated for 'chain 'N' and resid 85 through 87' Processing helix chain 'O' and resid 5 through 21 removed outlier: 5.133A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 59 No H-bonds generated for 'chain 'O' and resid 56 through 59' Processing helix chain 'O' and resid 68 through 85 removed outlier: 4.409A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 111 Processing helix chain 'P' and resid 7 through 11 Processing helix chain 'P' and resid 99 through 101 No H-bonds generated for 'chain 'P' and resid 99 through 101' Processing helix chain 'Q' and resid 6 through 20 removed outlier: 4.028A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA Q 20 " --> pdb=" O ILE Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 28 Processing helix chain 'Q' and resid 31 through 71 removed outlier: 4.287A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 84 Processing helix chain 'Q' and resid 91 through 99 removed outlier: 4.037A pdb=" N ALA Q 95 " --> pdb=" O ARG Q 91 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP Q 96 " --> pdb=" O LYS Q 92 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE Q 97 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 91 through 99' Processing helix chain 'Q' and resid 103 through 116 removed outlier: 3.534A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 16 No H-bonds generated for 'chain 'S' and resid 14 through 16' Processing helix chain 'S' and resid 18 through 21 No H-bonds generated for 'chain 'S' and resid 18 through 21' Processing helix chain 'S' and resid 32 through 38 removed outlier: 4.150A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 59 removed outlier: 3.502A pdb=" N VAL S 45 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 5 through 7 No H-bonds generated for 'chain 'T' and resid 5 through 7' Processing helix chain 'T' and resid 22 through 25 No H-bonds generated for 'chain 'T' and resid 22 through 25' Processing helix chain 'T' and resid 40 through 49 removed outlier: 3.529A pdb=" N ALA T 45 " --> pdb=" O GLU T 42 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS T 49 " --> pdb=" O ALA T 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'V' and resid 14 through 23 removed outlier: 4.014A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 52 Processing helix chain 'X' and resid 52 through 61 Processing helix chain 'X' and resid 63 through 73 removed outlier: 6.196A pdb=" N ALA X 68 " --> pdb=" O ASP X 64 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 21 Processing helix chain 'Y' and resid 28 through 33 Processing helix chain 'Y' and resid 41 through 59 removed outlier: 3.763A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG Y 47 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL Y 50 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 25 Processing helix chain 'Z' and resid 41 through 50 Processing sheet with id= A, first strand: chain '1' and resid 6 through 11 Processing sheet with id= B, first strand: chain '1' and resid 34 through 39 Processing sheet with id= C, first strand: chain '4' and resid 15 through 18 Processing sheet with id= D, first strand: chain '5' and resid 43 through 46 Processing sheet with id= E, first strand: chain '5' and resid 62 through 64 Processing sheet with id= F, first strand: chain '6' and resid 77 through 80 removed outlier: 7.305A pdb=" N GLU 6 40 " --> pdb=" O ALA 6 11 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU 6 13 " --> pdb=" O GLU 6 40 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU 6 42 " --> pdb=" O LEU 6 13 " (cutoff:3.500A) removed outlier: 12.470A pdb=" N HIS 6 15 " --> pdb=" O LEU 6 42 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N VAL 6 44 " --> pdb=" O HIS 6 15 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '6' and resid 200 through 203 removed outlier: 6.447A pdb=" N LEU 6 279 " --> pdb=" O SER 6 201 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL 6 203 " --> pdb=" O LEU 6 279 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU 6 281 " --> pdb=" O VAL 6 203 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '6' and resid 236 through 238 Processing sheet with id= I, first strand: chain '6' and resid 389 through 394 removed outlier: 6.104A pdb=" N GLN 6 403 " --> pdb=" O GLU 6 390 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLU 6 392 " --> pdb=" O SER 6 401 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER 6 401 " --> pdb=" O GLU 6 392 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '7' and resid 23 through 25 Processing sheet with id= K, first strand: chain 'C' and resid 91 through 95 removed outlier: 3.831A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 172 through 174 Processing sheet with id= M, first strand: chain 'D' and resid 4 through 7 Processing sheet with id= N, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.259A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 36 through 38 removed outlier: 3.550A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 128 through 130 Processing sheet with id= Q, first strand: chain 'G' and resid 15 through 19 Processing sheet with id= R, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.555A pdb=" N ARG G 94 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS G 114 " --> pdb=" O ILE G 102 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 120 through 123 Processing sheet with id= T, first strand: chain 'H' and resid 18 through 20 Processing sheet with id= U, first strand: chain 'I' and resid 9 through 13 Processing sheet with id= V, first strand: chain 'J' and resid 15 through 18 removed outlier: 7.068A pdb=" N TYR J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N VAL J 18 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE J 55 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 74 through 76 Processing sheet with id= X, first strand: chain 'K' and resid 58 through 61 Processing sheet with id= Y, first strand: chain 'K' and resid 68 through 70 Processing sheet with id= Z, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.787A pdb=" N MET K 6 " --> pdb=" O VAL K 18 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL K 18 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS K 39 " --> pdb=" O ILE K 21 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 75 through 77 removed outlier: 4.053A pdb=" N LYS L 109 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE L 77 " --> pdb=" O LYS L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'M' and resid 32 through 35 removed outlier: 3.598A pdb=" N VAL M 131 " --> pdb=" O GLY M 32 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.722A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 25 through 30 Processing sheet with id= AE, first strand: chain 'P' and resid 24 through 32 removed outlier: 3.654A pdb=" N GLY P 44 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE P 42 " --> pdb=" O VAL P 27 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'P' and resid 60 through 63 Processing sheet with id= AG, first strand: chain 'R' and resid 71 through 73 Processing sheet with id= AH, first strand: chain 'S' and resid 73 through 77 Processing sheet with id= AI, first strand: chain 'S' and resid 82 through 86 Processing sheet with id= AJ, first strand: chain 'T' and resid 30 through 33 Processing sheet with id= AK, first strand: chain 'U' and resid 82 through 84 Processing sheet with id= AL, first strand: chain 'V' and resid 38 through 43 removed outlier: 6.817A pdb=" N ILE V 89 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N TYR V 31 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE V 91 " --> pdb=" O TYR V 31 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 32 through 38 Processing sheet with id= AN, first strand: chain 'Z' and resid 34 through 38 698 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1910 hydrogen bonds 2782 hydrogen bond angles 0 basepair planarities 797 basepair parallelities 999 stacking parallelities Total time for adding SS restraints: 107.89 Time building geometry restraints manager: 60.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10775 1.32 - 1.44: 45652 1.44 - 1.57: 42916 1.57 - 1.69: 6044 1.69 - 1.82: 186 Bond restraints: 105573 Sorted by residual: bond pdb=" N3B GNP 6 527 " pdb=" PG GNP 6 527 " ideal model delta sigma weight residual 1.801 1.568 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" O3A GNP 6 527 " pdb=" PB GNP 6 527 " ideal model delta sigma weight residual 1.687 1.498 0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C SER C 271 " pdb=" N LYS C 272 " ideal model delta sigma weight residual 1.329 1.224 0.105 1.40e-02 5.10e+03 5.60e+01 bond pdb=" C ILE U 102 " pdb=" N LYS U 103 " ideal model delta sigma weight residual 1.329 1.225 0.104 1.40e-02 5.10e+03 5.47e+01 bond pdb=" C LEU T 93 " pdb=" N ASP T 94 " ideal model delta sigma weight residual 1.329 1.226 0.103 1.40e-02 5.10e+03 5.43e+01 ... (remaining 105568 not shown) Histogram of bond angle deviations from ideal: 95.84 - 104.48: 13048 104.48 - 113.12: 67353 113.12 - 121.75: 52393 121.75 - 130.39: 23322 130.39 - 139.03: 1425 Bond angle restraints: 157541 Sorted by residual: angle pdb=" C LEU 6 372 " pdb=" N PRO 6 373 " pdb=" CA PRO 6 373 " ideal model delta sigma weight residual 120.38 134.42 -14.04 1.03e+00 9.43e-01 1.86e+02 angle pdb=" N PHE J 4 " pdb=" CA PHE J 4 " pdb=" C PHE J 4 " ideal model delta sigma weight residual 111.71 98.72 12.99 1.34e+00 5.57e-01 9.40e+01 angle pdb=" C PHE V 26 " pdb=" N PRO V 27 " pdb=" CA PRO V 27 " ideal model delta sigma weight residual 119.78 129.18 -9.40 1.03e+00 9.43e-01 8.33e+01 angle pdb=" N GLY 3 52 " pdb=" CA GLY 3 52 " pdb=" C GLY 3 52 " ideal model delta sigma weight residual 115.66 101.64 14.02 1.56e+00 4.11e-01 8.08e+01 angle pdb=" N THR T 29 " pdb=" CA THR T 29 " pdb=" C THR T 29 " ideal model delta sigma weight residual 110.53 121.89 -11.36 1.32e+00 5.74e-01 7.40e+01 ... (remaining 157536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 57247 36.00 - 72.00: 6788 72.00 - 107.99: 947 107.99 - 143.99: 45 143.99 - 179.99: 48 Dihedral angle restraints: 65075 sinusoidal: 53167 harmonic: 11908 Sorted by residual: dihedral pdb=" C5' G B2252 " pdb=" C4' G B2252 " pdb=" C3' G B2252 " pdb=" O3' G B2252 " ideal model delta sinusoidal sigma weight residual 147.00 73.44 73.56 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C4' G B2252 " pdb=" C3' G B2252 " pdb=" C2' G B2252 " pdb=" C1' G B2252 " ideal model delta sinusoidal sigma weight residual -35.00 34.24 -69.24 1 8.00e+00 1.56e-02 9.68e+01 dihedral pdb=" C4' U B1779 " pdb=" C3' U B1779 " pdb=" C2' U B1779 " pdb=" C1' U B1779 " ideal model delta sinusoidal sigma weight residual -35.00 34.15 -69.15 1 8.00e+00 1.56e-02 9.66e+01 ... (remaining 65072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 18159 0.094 - 0.189: 1844 0.189 - 0.283: 105 0.283 - 0.378: 4 0.378 - 0.472: 3 Chirality restraints: 20115 Sorted by residual: chirality pdb=" CA GLN 6 20 " pdb=" N GLN 6 20 " pdb=" C GLN 6 20 " pdb=" CB GLN 6 20 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" C3' G B2252 " pdb=" C4' G B2252 " pdb=" O3' G B2252 " pdb=" C2' G B2252 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" C3' U B1779 " pdb=" C4' U B1779 " pdb=" O3' U B1779 " pdb=" C2' U B1779 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.39 2.00e-01 2.50e+01 3.72e+00 ... (remaining 20112 not shown) Planarity restraints: 8752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE W 25 " -0.025 2.00e-02 2.50e+03 2.44e-02 1.04e+01 pdb=" CG PHE W 25 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE W 25 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE W 25 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE W 25 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE W 25 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE W 25 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 97 " 0.035 2.00e-02 2.50e+03 2.24e-02 1.00e+01 pdb=" CG TYR P 97 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR P 97 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR P 97 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR P 97 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR P 97 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR P 97 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR P 97 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B1395 " 0.032 2.00e-02 2.50e+03 1.80e-02 8.91e+00 pdb=" N9 A B1395 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A B1395 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B1395 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B1395 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A B1395 " 0.020 2.00e-02 2.50e+03 pdb=" N6 A B1395 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B1395 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A B1395 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B1395 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A B1395 " 0.001 2.00e-02 2.50e+03 ... (remaining 8749 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 134 2.09 - 2.79: 30201 2.79 - 3.50: 174023 3.50 - 4.20: 308728 4.20 - 4.90: 409968 Nonbonded interactions: 923054 Sorted by model distance: nonbonded pdb=" CG PRO H 32 " pdb=" CG TRP X 38 " model vdw 1.391 3.660 nonbonded pdb=" O ARG 5 134 " pdb=" N LEU 5 136 " model vdw 1.460 2.520 nonbonded pdb=" CG PRO H 32 " pdb=" CB TRP X 38 " model vdw 1.495 3.840 nonbonded pdb=" CG1 VAL 6 365 " pdb=" CZ ARG 6 405 " model vdw 1.539 3.690 nonbonded pdb=" O ALA 6 366 " pdb=" O GLN 6 367 " model vdw 1.581 3.040 ... (remaining 923049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.010 Normalize map: mean=0, sd=1: 1.230 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: 0.090 Extract box with map and model: 9.600 Check model and map are aligned: 1.120 Set scattering table: 0.650 Process input model: 316.810 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 334.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 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 : 0.011 0.233 105573 Z= 0.672 Angle : 1.275 16.032 157541 Z= 0.734 Chirality : 0.057 0.472 20115 Planarity : 0.006 0.064 8752 Dihedral : 24.173 179.989 57397 Min Nonbonded Distance : 1.391 Molprobity Statistics. All-atom Clashscore : 57.89 Ramachandran Plot: Outliers : 6.67 % Allowed : 11.68 % Favored : 81.65 % Rotamer: Outliers : 0.21 % Allowed : 1.24 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.35 (0.12), residues: 4126 helix: -3.40 (0.10), residues: 988 sheet: -3.77 (0.17), residues: 524 loop : -1.37 (0.13), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP E 78 HIS 0.014 0.004 HIS 2 16 PHE 0.056 0.004 PHE W 25 TYR 0.051 0.004 TYR P 97 ARG 0.021 0.002 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1071 time to evaluate : 4.290 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 outliers start: 7 outliers final: 3 residues processed: 1076 average time/residue: 1.0148 time to fit residues: 1795.7041 Evaluate side-chains 574 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 571 time to evaluate : 4.306 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.7197 time to fit residues: 8.6972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 596 optimal weight: 6.9990 chunk 535 optimal weight: 7.9990 chunk 296 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 360 optimal weight: 3.9990 chunk 285 optimal weight: 10.0000 chunk 553 optimal weight: 0.1980 chunk 214 optimal weight: 5.9990 chunk 336 optimal weight: 20.0000 chunk 411 optimal weight: 9.9990 chunk 641 optimal weight: 8.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 2 13 ASN 3 23 HIS 3 42 HIS 4 33 HIS ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 43 GLN 6 82 HIS 6 146 GLN ** 6 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 355 GLN 6 367 GLN ** 7 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 148 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN E 29 HIS ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN F 4 HIS F 22 ASN G 115 GLN G 138 GLN H 18 GLN I 5 GLN I 18 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN N 81 ASN P 11 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 11 GLN R 86 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN T 28 ASN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN U 98 ASN V 51 GLN ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Z 19 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 105573 Z= 0.256 Angle : 0.849 15.580 157541 Z= 0.425 Chirality : 0.042 0.366 20115 Planarity : 0.006 0.082 8752 Dihedral : 24.863 179.897 49298 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 26.72 Ramachandran Plot: Outliers : 1.72 % Allowed : 11.46 % Favored : 86.82 % Rotamer: Outliers : 0.32 % Allowed : 4.19 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.51 (0.12), residues: 4126 helix: -2.20 (0.13), residues: 1053 sheet: -3.31 (0.17), residues: 573 loop : -2.18 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP X 38 HIS 0.015 0.002 HIS Q 13 PHE 0.035 0.003 PHE W 25 TYR 0.036 0.003 TYR 6 205 ARG 0.038 0.001 ARG G 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 839 time to evaluate : 4.424 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 outliers start: 11 outliers final: 5 residues processed: 848 average time/residue: 0.9581 time to fit residues: 1373.4481 Evaluate side-chains 533 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 528 time to evaluate : 4.340 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.7117 time to fit residues: 11.5165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 356 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 533 optimal weight: 40.0000 chunk 436 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 642 optimal weight: 0.0010 chunk 693 optimal weight: 6.9990 chunk 572 optimal weight: 5.9990 chunk 636 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 chunk 515 optimal weight: 50.0000 overall best weight: 7.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 HIS ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN 4 33 HIS ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN ** 6 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 368 HIS ** 7 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN G 63 GLN H 18 GLN I 18 ASN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN P 55 HIS ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN Q 71 ASN R 6 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 ASN U 39 ASN ** Y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.207 105573 Z= 0.336 Angle : 0.852 13.825 157541 Z= 0.428 Chirality : 0.043 0.471 20115 Planarity : 0.007 0.103 8752 Dihedral : 24.679 179.784 49298 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 31.23 Ramachandran Plot: Outliers : 1.53 % Allowed : 12.97 % Favored : 85.51 % Rotamer: Outliers : 0.15 % Allowed : 5.55 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -3.53 (0.12), residues: 4126 helix: -1.88 (0.14), residues: 1040 sheet: -3.09 (0.17), residues: 633 loop : -2.41 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.005 TRP 6 341 HIS 0.020 0.002 HIS J 80 PHE 0.040 0.003 PHE H 29 TYR 0.052 0.003 TYR 3 63 ARG 0.026 0.001 ARG H 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 749 time to evaluate : 4.414 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 outliers start: 5 outliers final: 1 residues processed: 753 average time/residue: 0.9590 time to fit residues: 1224.6523 Evaluate side-chains 528 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 527 time to evaluate : 4.360 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7293 time to fit residues: 6.0465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 634 optimal weight: 8.9990 chunk 482 optimal weight: 30.0000 chunk 333 optimal weight: 50.0000 chunk 71 optimal weight: 7.9990 chunk 306 optimal weight: 30.0000 chunk 431 optimal weight: 7.9990 chunk 644 optimal weight: 9.9990 chunk 682 optimal weight: 30.0000 chunk 336 optimal weight: 30.0000 chunk 610 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN ** 5 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 GLN ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.6947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 105573 Z= 0.315 Angle : 0.778 13.919 157541 Z= 0.395 Chirality : 0.041 0.362 20115 Planarity : 0.006 0.083 8752 Dihedral : 24.559 179.669 49298 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 29.61 Ramachandran Plot: Outliers : 1.36 % Allowed : 11.92 % Favored : 86.72 % Rotamer: Outliers : 0.12 % Allowed : 3.63 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.44 (0.12), residues: 4126 helix: -1.59 (0.15), residues: 1030 sheet: -2.87 (0.18), residues: 615 loop : -2.51 (0.11), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP T 80 HIS 0.015 0.002 HIS T 70 PHE 0.030 0.003 PHE 6 111 TYR 0.031 0.003 TYR 6 205 ARG 0.019 0.001 ARG X 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 723 time to evaluate : 4.482 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: 4 outliers final: 2 residues processed: 727 average time/residue: 0.9673 time to fit residues: 1198.3655 Evaluate side-chains 537 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 535 time to evaluate : 4.411 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7107 time to fit residues: 7.8002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 568 optimal weight: 30.0000 chunk 387 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 508 optimal weight: 0.8980 chunk 281 optimal weight: 20.0000 chunk 582 optimal weight: 3.9990 chunk 471 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 348 optimal weight: 20.0000 chunk 612 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 overall best weight: 10.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 126 GLN ** 5 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 HIS J 47 HIS ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.8100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 105573 Z= 0.359 Angle : 0.839 15.781 157541 Z= 0.422 Chirality : 0.044 0.347 20115 Planarity : 0.007 0.143 8752 Dihedral : 24.603 179.963 49298 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 35.01 Ramachandran Plot: Outliers : 1.28 % Allowed : 13.98 % Favored : 84.73 % Rotamer: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.43 (0.12), residues: 4126 helix: -1.43 (0.15), residues: 1011 sheet: -2.87 (0.18), residues: 616 loop : -2.58 (0.11), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP T 80 HIS 0.023 0.002 HIS J 47 PHE 0.036 0.003 PHE J 4 TYR 0.022 0.003 TYR J 44 ARG 0.015 0.001 ARG 4 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 680 time to evaluate : 4.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 2 residues processed: 682 average time/residue: 1.0236 time to fit residues: 1201.1488 Evaluate side-chains 508 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 506 time to evaluate : 4.476 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7298 time to fit residues: 7.6563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 229 optimal weight: 20.0000 chunk 614 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 400 optimal weight: 30.0000 chunk 168 optimal weight: 20.0000 chunk 683 optimal weight: 30.0000 chunk 567 optimal weight: 3.9990 chunk 316 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 225 optimal weight: 30.0000 chunk 358 optimal weight: 20.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 5 ASN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 126 GLN ** 6 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 91 ASN ** 6 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN H 18 GLN H 73 ASN H 145 ASN I 30 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.8711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 105573 Z= 0.314 Angle : 0.764 13.999 157541 Z= 0.387 Chirality : 0.041 0.341 20115 Planarity : 0.006 0.077 8752 Dihedral : 24.533 179.948 49298 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 30.71 Ramachandran Plot: Outliers : 1.28 % Allowed : 12.00 % Favored : 86.72 % Rotamer: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.12), residues: 4126 helix: -1.38 (0.15), residues: 1021 sheet: -2.77 (0.18), residues: 593 loop : -2.62 (0.11), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP E 78 HIS 0.018 0.002 HIS R 12 PHE 0.048 0.003 PHE Q 56 TYR 0.033 0.003 TYR X 77 ARG 0.021 0.001 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 669 time to evaluate : 4.464 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 outliers start: 1 outliers final: 1 residues processed: 670 average time/residue: 0.9450 time to fit residues: 1088.4833 Evaluate side-chains 510 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 509 time to evaluate : 4.358 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7672 time to fit residues: 6.0735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 658 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 389 optimal weight: 20.0000 chunk 498 optimal weight: 7.9990 chunk 386 optimal weight: 20.0000 chunk 575 optimal weight: 8.9990 chunk 381 optimal weight: 20.0000 chunk 680 optimal weight: 0.9980 chunk 425 optimal weight: 20.0000 chunk 414 optimal weight: 3.9990 chunk 314 optimal weight: 20.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 5 ASN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 355 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN I 30 GLN J 136 GLN ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.9046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 105573 Z= 0.225 Angle : 0.683 9.980 157541 Z= 0.346 Chirality : 0.037 0.335 20115 Planarity : 0.005 0.075 8752 Dihedral : 24.363 179.908 49298 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 25.95 Ramachandran Plot: Outliers : 1.19 % Allowed : 12.09 % Favored : 86.72 % Rotamer: Outliers : 0.03 % Allowed : 1.51 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.12), residues: 4126 helix: -1.10 (0.16), residues: 1031 sheet: -2.56 (0.19), residues: 594 loop : -2.57 (0.11), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP G 61 HIS 0.012 0.002 HIS J 47 PHE 0.026 0.002 PHE M 117 TYR 0.022 0.002 TYR F 6 ARG 0.010 0.001 ARG W 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 683 time to evaluate : 4.476 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 outliers start: 1 outliers final: 0 residues processed: 684 average time/residue: 0.9712 time to fit residues: 1145.4212 Evaluate side-chains 517 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 517 time to evaluate : 4.449 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 420 optimal weight: 30.0000 chunk 271 optimal weight: 20.0000 chunk 406 optimal weight: 10.0000 chunk 204 optimal weight: 40.0000 chunk 133 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 432 optimal weight: 2.9990 chunk 463 optimal weight: 9.9990 chunk 336 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 chunk 534 optimal weight: 0.0570 overall best weight: 6.6108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 5 ASN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 355 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 HIS ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.9340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 105573 Z= 0.235 Angle : 0.676 9.505 157541 Z= 0.343 Chirality : 0.037 0.339 20115 Planarity : 0.005 0.079 8752 Dihedral : 24.280 179.583 49298 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 26.72 Ramachandran Plot: Outliers : 1.21 % Allowed : 11.71 % Favored : 87.08 % Rotamer: Outliers : 0.03 % Allowed : 1.12 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.12), residues: 4126 helix: -0.98 (0.16), residues: 1030 sheet: -2.49 (0.18), residues: 610 loop : -2.56 (0.11), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP T 80 HIS 0.009 0.002 HIS J 47 PHE 0.032 0.002 PHE S 75 TYR 0.016 0.002 TYR 6 56 ARG 0.015 0.001 ARG K 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 651 time to evaluate : 4.375 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 outliers start: 1 outliers final: 0 residues processed: 652 average time/residue: 0.9294 time to fit residues: 1048.7107 Evaluate side-chains 495 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 4.422 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 618 optimal weight: 9.9990 chunk 651 optimal weight: 10.0000 chunk 594 optimal weight: 0.0970 chunk 634 optimal weight: 0.3980 chunk 381 optimal weight: 20.0000 chunk 276 optimal weight: 20.0000 chunk 497 optimal weight: 7.9990 chunk 194 optimal weight: 20.0000 chunk 573 optimal weight: 9.9990 chunk 599 optimal weight: 6.9990 chunk 631 optimal weight: 8.9990 overall best weight: 4.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 5 ASN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 355 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN P 55 HIS Q 55 GLN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 HIS ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.9620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 105573 Z= 0.190 Angle : 0.631 10.109 157541 Z= 0.320 Chirality : 0.035 0.328 20115 Planarity : 0.005 0.079 8752 Dihedral : 24.126 179.796 49298 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 23.00 Ramachandran Plot: Outliers : 1.19 % Allowed : 11.15 % Favored : 87.66 % Rotamer: Outliers : 0.06 % Allowed : 0.83 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.12), residues: 4126 helix: -0.83 (0.16), residues: 1033 sheet: -2.23 (0.19), residues: 604 loop : -2.49 (0.11), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 247 HIS 0.010 0.001 HIS J 47 PHE 0.026 0.002 PHE Q 56 TYR 0.030 0.002 TYR 7 84 ARG 0.009 0.001 ARG M 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 655 time to evaluate : 5.288 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 outliers start: 2 outliers final: 1 residues processed: 657 average time/residue: 0.9347 time to fit residues: 1071.2460 Evaluate side-chains 523 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 522 time to evaluate : 4.458 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.8249 time to fit residues: 6.3287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7529 > 50: distance: 55 - 61: 9.013 distance: 61 - 62: 16.991 distance: 62 - 63: 14.009 distance: 62 - 65: 12.590 distance: 63 - 64: 19.954 distance: 63 - 70: 19.568 distance: 65 - 66: 8.845 distance: 66 - 67: 20.907 distance: 67 - 68: 18.729 distance: 68 - 69: 4.033 distance: 70 - 71: 19.256 distance: 71 - 72: 18.720 distance: 71 - 74: 15.742 distance: 72 - 73: 48.828 distance: 72 - 75: 32.738 distance: 79 - 80: 26.406 distance: 80 - 81: 13.605 distance: 80 - 83: 6.321 distance: 81 - 82: 34.068 distance: 81 - 87: 12.723 distance: 83 - 84: 10.167 distance: 84 - 85: 11.935 distance: 84 - 86: 37.863 distance: 87 - 88: 8.231 distance: 88 - 89: 10.446 distance: 88 - 91: 15.128 distance: 89 - 90: 40.883 distance: 89 - 96: 10.101 distance: 91 - 92: 25.822 distance: 92 - 93: 22.038 distance: 93 - 94: 12.264 distance: 93 - 95: 10.831 distance: 96 - 97: 23.415 distance: 97 - 98: 6.337 distance: 97 - 100: 8.365 distance: 98 - 99: 12.232 distance: 98 - 104: 10.123 distance: 100 - 101: 18.194 distance: 100 - 102: 29.601 distance: 101 - 103: 8.794 distance: 105 - 106: 16.337 distance: 105 - 108: 17.134 distance: 106 - 107: 18.928 distance: 106 - 113: 28.160 distance: 108 - 109: 15.152 distance: 109 - 110: 34.227 distance: 110 - 111: 16.139 distance: 110 - 112: 10.473 distance: 113 - 114: 8.345 distance: 114 - 115: 4.969 distance: 114 - 117: 17.473 distance: 115 - 116: 22.957 distance: 117 - 118: 46.235 distance: 119 - 120: 42.180 distance: 120 - 121: 39.772 distance: 121 - 122: 16.677 distance: 121 - 123: 56.964 distance: 123 - 124: 42.112 distance: 124 - 127: 18.049 distance: 125 - 126: 13.587 distance: 125 - 130: 29.466 distance: 127 - 128: 40.781 distance: 127 - 129: 33.691