Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 09:33:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/05_2023/5ady_3133_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/05_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_3133/05_2023/5ady_3133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/05_2023/5ady_3133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/05_2023/5ady_3133_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/05_2023/5ady_3133_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.040 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 38.80, per 1000 atoms: 0.40 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: 56.25 Conformation dependent library (CDL) restraints added in 4.6 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: 41.51 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: 104.22 Time building geometry restraints manager: 59.45 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: 53163 36.00 - 72.00: 3061 72.00 - 107.99: 316 107.99 - 143.99: 45 143.99 - 179.99: 48 Dihedral angle restraints: 56633 sinusoidal: 44725 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 56630 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: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 12.570 Check model and map are aligned: 1.080 Set scattering table: 0.620 Process input model: 305.270 Find NCS groups from input model: 1.660 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:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 325.460 ------------------------------------------------------------------------------- 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 : 18.750 179.989 48955 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 % 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 *********************** 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 : 4.439 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: 1.0196 time to fit residues: 1803.0815 Evaluate side-chains 574 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 571 time to evaluate : 4.547 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.7127 time to fit residues: 8.8932 ------------------------------------------------------------------------------- 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: 4.9990 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: 5.9990 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 ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 10 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** 6 355 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 22 ASN G 115 GLN G 138 GLN H 18 GLN I 5 GLN I 18 ASN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** R 6 GLN R 11 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: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.3388 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: