Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 05:47:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syn_25534/04_2023/7syn_25534.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syn_25534/04_2023/7syn_25534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syn_25534/04_2023/7syn_25534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syn_25534/04_2023/7syn_25534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syn_25534/04_2023/7syn_25534.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syn_25534/04_2023/7syn_25534.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Zn 2 6.06 5 P 1858 5.49 5 S 180 5.16 5 C 42397 2.51 5 N 14495 2.21 5 O 19829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 126": "OD1" <-> "OD2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 40": "OE1" <-> "OE2" Residue "F ASP 143": "OD1" <-> "OD2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 171": "OE1" <-> "OE2" Residue "G ASP 175": "OD1" <-> "OD2" Residue "G TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 208": "OE1" <-> "OE2" Residue "I ASP 35": "OD1" <-> "OD2" Residue "I ASP 127": "OD1" <-> "OD2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 61": "OD1" <-> "OD2" Residue "K ASP 26": "OD1" <-> "OD2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "K ASP 158": "OD1" <-> "OD2" Residue "K TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 103": "OE1" <-> "OE2" Residue "M PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 86": "OE1" <-> "OE2" Residue "O ASP 108": "OD1" <-> "OD2" Residue "O GLU 142": "OE1" <-> "OE2" Residue "P PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "R ASP 101": "OD1" <-> "OD2" Residue "R TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 101": "OD1" <-> "OD2" Residue "T GLU 7": "OE1" <-> "OE2" Residue "T GLU 65": "OE1" <-> "OE2" Residue "T PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 8": "OD1" <-> "OD2" Residue "V GLU 72": "OE1" <-> "OE2" Residue "W TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "Y GLU 53": "OE1" <-> "OE2" Residue "Y GLU 99": "OE1" <-> "OE2" Residue "Y GLU 139": "OE1" <-> "OE2" Residue "Z ASP 53": "OD1" <-> "OD2" Residue "Z PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 86": "OE1" <-> "OE2" Residue "Z TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 98": "OE1" <-> "OE2" Residue "a GLU 61": "OE1" <-> "OE2" Residue "a GLU 75": "OE1" <-> "OE2" Residue "b GLU 90": "OE1" <-> "OE2" Residue "c GLU 13": "OE1" <-> "OE2" Residue "c PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 231": "OD1" <-> "OD2" Residue "h TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 268": "OD1" <-> "OD2" Residue "h ASP 304": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 78761 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 143, 'rna2p_pyr': 113, 'rna3p_pur': 754, 'rna3p_pyr': 687} Link IDs: {'rna2p': 255, 'rna3p': 1441} Chain breaks: 11 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 956 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "z" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3465 Classifications: {'RNA': 162} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 73, 'rna3p_pyr': 64} Link IDs: {'rna2p': 24, 'rna3p': 137} Chain breaks: 1 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69331 SG CYS b 23 92.888 128.480 132.515 1.00 40.42 S ATOM 69352 SG CYS b 26 95.819 129.317 135.400 1.00 46.80 S ATOM 69735 SG CYS b 74 95.119 126.037 134.169 1.00 39.58 S ATOM 69754 SG CYS b 77 95.025 128.105 135.939 1.00 41.97 S ATOM 72396 SG CYS g 121 141.261 111.137 244.385 1.00128.07 S ATOM 72432 SG CYS g 126 139.659 108.910 242.798 1.00135.44 S ATOM 72550 SG CYS g 141 141.802 112.282 240.878 1.00152.31 S ATOM 72569 SG CYS g 144 138.910 111.855 241.491 1.00150.33 S Time building chain proxies: 32.72, per 1000 atoms: 0.42 Number of scatterers: 78761 At special positions: 0 Unit cell: (236.55, 195.7, 264.1, 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) Zn 2 29.99 S 180 16.00 P 1858 15.00 O 19829 8.00 N 14495 7.00 C 42397 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=0, symmetry=0 Time building additional restraints: 32.27 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " Number of angles added : 12 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9066 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 60 sheets defined 35.2% alpha, 17.8% beta 477 base pairs and 878 stacking pairs defined. Time for finding SS restraints: 22.07 Creating SS restraints... Processing helix chain 'B' and resid 12 through 22 removed outlier: 3.970A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 50 through 68 removed outlier: 3.673A pdb=" N THR B 54 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.822A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.633A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 157 through 175 Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.576A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.960A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 232 through 245 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.658A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 removed outlier: 6.102A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 54 through 60 removed outlier: 3.521A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 60' Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 97 through 111 removed outlier: 3.588A pdb=" N GLN E 101 " --> pdb=" O CYS E 97 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY E 111 " --> pdb=" O TYR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 130 removed outlier: 3.868A pdb=" N GLY E 130 " --> pdb=" O ILE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 37 through 41 removed outlier: 3.838A pdb=" N CYS F 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 59 through 67 Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 223 through 225 No H-bonds generated for 'chain 'F' and resid 223 through 225' Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 67 through 75 removed outlier: 3.535A pdb=" N SER G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 removed outlier: 3.707A pdb=" N THR G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 118 removed outlier: 3.506A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN G 114 " --> pdb=" O GLN G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 173 Processing helix chain 'G' and resid 173 through 178 removed outlier: 3.526A pdb=" N ILE G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 183 Processing helix chain 'G' and resid 187 through 203 removed outlier: 4.191A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 28 removed outlier: 3.619A pdb=" N TYR H 28 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 236 Processing helix chain 'I' and resid 17 through 34 Processing helix chain 'I' and resid 36 through 40 Processing helix chain 'I' and resid 68 through 73 Processing helix chain 'I' and resid 75 through 87 removed outlier: 4.021A pdb=" N VAL I 80 " --> pdb=" O GLN I 76 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.972A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.969A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 118 Processing helix chain 'J' and resid 132 through 139 removed outlier: 3.737A pdb=" N LEU J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.708A pdb=" N LYS J 148 " --> pdb=" O LYS J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 178 through 183 removed outlier: 3.613A pdb=" N CYS J 182 " --> pdb=" O ARG J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 207 Processing helix chain 'K' and resid 21 through 36 removed outlier: 3.618A pdb=" N LEU K 25 " --> pdb=" O GLU K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.239A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 85 Processing helix chain 'K' and resid 93 through 100 Processing helix chain 'K' and resid 101 through 107 Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 172 through 186 removed outlier: 3.827A pdb=" N LYS K 176 " --> pdb=" O ARG K 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 17 removed outlier: 3.514A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 Processing helix chain 'L' and resid 72 through 84 Processing helix chain 'M' and resid 48 through 53 Processing helix chain 'N' and resid 15 through 29 Processing helix chain 'N' and resid 34 through 44 Processing helix chain 'N' and resid 60 through 70 removed outlier: 3.701A pdb=" N LEU N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 90 Processing helix chain 'N' and resid 119 through 130 removed outlier: 4.225A pdb=" N VAL N 123 " --> pdb=" O GLN N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 44 removed outlier: 3.781A pdb=" N VAL O 33 " --> pdb=" O THR O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 57 removed outlier: 3.648A pdb=" N GLY O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL O 52 " --> pdb=" O SER O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 67 removed outlier: 3.999A pdb=" N VAL O 66 " --> pdb=" O GLN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 105 removed outlier: 4.349A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN O 105 " --> pdb=" O HIS O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 132 Processing helix chain 'P' and resid 58 through 62 removed outlier: 3.583A pdb=" N VAL P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 62' Processing helix chain 'P' and resid 64 through 68 Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 110 through 122 removed outlier: 4.164A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.954A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 47 removed outlier: 3.965A pdb=" N ARG Q 47 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'Q' and resid 86 through 90 Processing helix chain 'Q' and resid 108 through 112 removed outlier: 4.093A pdb=" N ILE Q 112 " --> pdb=" O PRO Q 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'R' and resid 47 through 59 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 60 through 65 removed outlier: 4.155A pdb=" N GLY R 65 " --> pdb=" O GLU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.658A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.854A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 27 through 39 Processing helix chain 'S' and resid 44 through 64 Processing helix chain 'S' and resid 75 through 84 Processing helix chain 'S' and resid 99 through 108 removed outlier: 3.651A pdb=" N LEU S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.784A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 removed outlier: 3.597A pdb=" N VAL T 64 " --> pdb=" O THR T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.591A pdb=" N TYR T 77 " --> pdb=" O PRO T 74 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 74 through 78' Processing helix chain 'T' and resid 80 through 84 removed outlier: 3.555A pdb=" N PHE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 10 through 26 removed outlier: 3.709A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 37 removed outlier: 4.511A pdb=" N ASP U 35 " --> pdb=" O GLU U 32 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL U 37 " --> pdb=" O VAL U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 72 through 79 Processing helix chain 'U' and resid 97 through 110 Processing helix chain 'U' and resid 124 through 143 Processing helix chain 'V' and resid 28 through 46 removed outlier: 3.779A pdb=" N LEU V 32 " --> pdb=" O ASN V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 103 removed outlier: 3.801A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.652A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 77 Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 45 Processing helix chain 'X' and resid 85 through 94 removed outlier: 3.592A pdb=" N ASN X 92 " --> pdb=" O LYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 119 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 32 through 39 removed outlier: 4.023A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 90 through 94 Processing helix chain 'Y' and resid 130 through 136 Processing helix chain 'Z' and resid 36 through 49 Processing helix chain 'Z' and resid 51 through 53 No H-bonds generated for 'chain 'Z' and resid 51 through 53' Processing helix chain 'Z' and resid 78 through 85 Processing helix chain 'Z' and resid 87 through 95 removed outlier: 3.695A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 116 Processing helix chain 'Z' and resid 120 through 125 removed outlier: 4.089A pdb=" N ASN Z 124 " --> pdb=" O THR Z 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 62 Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 94 Processing helix chain 'b' and resid 48 through 56 removed outlier: 4.636A pdb=" N ASP b 52 " --> pdb=" O ALA b 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'c' and resid 11 through 18 Processing helix chain 'e' and resid 3 through 8 removed outlier: 4.418A pdb=" N TRP e 8 " --> pdb=" O GLN e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 36 Processing helix chain 'e' and resid 40 through 46 Processing helix chain 'e' and resid 46 through 51 removed outlier: 3.680A pdb=" N ILE e 50 " --> pdb=" O TYR e 46 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 105 through 115 removed outlier: 4.100A pdb=" N GLN f 110 " --> pdb=" O LYS f 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 105 Processing helix chain 'n' and resid 2 through 25 Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.008A pdb=" N ILE B 48 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.334A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 147 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.686A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 13.418A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.299A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 216 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 123 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 67 removed outlier: 3.501A pdb=" N LEU C 86 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 13.418A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.299A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 216 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE C 142 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP C 209 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 104 through 116 removed outlier: 5.544A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 127 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 137 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.742A pdb=" N VAL D 205 " --> pdb=" O CYS D 222 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D 224 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 34 through 40 removed outlier: 3.505A pdb=" N ILE E 49 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU E 85 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE E 48 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU E 89 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 150 through 155 removed outlier: 3.704A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET E 189 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 137 " --> pdb=" O LYS E 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 155 removed outlier: 3.704A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET E 189 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 137 " --> pdb=" O LYS E 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 223 through 226 removed outlier: 6.698A pdb=" N VAL h 176 " --> pdb=" O LYS h 185 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN h 187 " --> pdb=" O VAL h 174 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL h 174 " --> pdb=" O ASN h 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB3, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.511A pdb=" N ILE F 92 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU F 97 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.209A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.508A pdb=" N LYS F 122 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 159 " --> pdb=" O ILE F 173 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 217 through 221 removed outlier: 6.799A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 229 through 230 removed outlier: 3.516A pdb=" N LYS F 230 " --> pdb=" O LYS F 233 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS F 233 " --> pdb=" O LYS F 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 123 through 126 removed outlier: 8.699A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE d 42 " --> pdb=" O VAL d 32 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N CYS d 27 " --> pdb=" O GLY d 19 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY d 19 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR d 15 " --> pdb=" O ARG d 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 12 through 17 removed outlier: 6.515A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 12 through 17 removed outlier: 6.770A pdb=" N ASN H 56 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.813A pdb=" N LYS H 93 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 160 through 164 removed outlier: 3.549A pdb=" N LYS H 160 " --> pdb=" O LYS H 172 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LYS H 164 " --> pdb=" O LYS H 168 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS H 168 " --> pdb=" O LYS H 164 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 48 through 52 removed outlier: 3.658A pdb=" N ILE I 51 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA I 59 " --> pdb=" O ILE I 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 185 through 188 removed outlier: 8.394A pdb=" N ASN I 186 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE I 154 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLU I 188 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL I 156 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU I 153 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE I 144 " --> pdb=" O LEU I 153 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS I 155 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS I 142 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS I 157 " --> pdb=" O VAL I 140 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL I 146 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE X 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL X 25 " --> pdb=" O VAL X 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 42 through 47 removed outlier: 6.680A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 62 through 66 removed outlier: 3.519A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG J 74 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG J 77 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU J 103 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL J 81 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE J 101 " --> pdb=" O VAL J 81 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.643A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 20 through 24 removed outlier: 3.693A pdb=" N ALA L 23 " --> pdb=" O PHE L 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 72 through 79 removed outlier: 6.981A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS M 144 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 91 through 96 removed outlier: 4.035A pdb=" N ARG M 101 " --> pdb=" O ILE M 96 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 31 through 32 removed outlier: 3.588A pdb=" N VAL N 110 " --> pdb=" O ALA N 32 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 52 through 53 removed outlier: 7.153A pdb=" N LEU N 52 " --> pdb=" O VAL N 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'P' and resid 52 through 57 removed outlier: 7.345A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR P 40 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP P 39 " --> pdb=" O SER P 36 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE P 95 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE P 129 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU P 97 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP P 131 " --> pdb=" O LEU P 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 76 through 78 removed outlier: 6.073A pdb=" N VAL Q 76 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR Q 97 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR Q 78 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR Q 101 " --> pdb=" O ASN Q 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 12 through 15 removed outlier: 7.020A pdb=" N LYS R 33 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N VAL R 72 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 97 through 98 removed outlier: 3.984A pdb=" N VAL S 98 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'T' and resid 12 through 15 Processing sheet with id=AE1, first strand: chain 'U' and resid 81 through 83 removed outlier: 3.904A pdb=" N GLY U 81 " --> pdb=" O SER U 93 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER U 93 " --> pdb=" O GLY U 81 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS U 91 " --> pdb=" O GLN U 83 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE3, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.557A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 54 through 55 removed outlier: 4.038A pdb=" N THR V 25 " --> pdb=" O GLU V 111 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU V 111 " --> pdb=" O THR V 25 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 15 through 16 removed outlier: 4.145A pdb=" N ARG W 15 " --> pdb=" O ILE W 24 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 32 through 39 removed outlier: 4.094A pdb=" N GLU W 38 " --> pdb=" O GLN W 49 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.772A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE X 130 " --> pdb=" O LYS X 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE X 128 " --> pdb=" O GLY X 73 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.772A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE X 130 " --> pdb=" O LYS X 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE X 128 " --> pdb=" O GLY X 73 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET X 111 " --> pdb=" O LEU X 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 128 through 129 removed outlier: 5.039A pdb=" N VAL Y 122 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA Y 103 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS Y 124 " --> pdb=" O LEU Y 101 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 10.855A pdb=" N PHE Y 120 " --> pdb=" O LYS Y 80 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR Y 82 " --> pdb=" O PHE Y 120 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL Y 122 " --> pdb=" O THR Y 82 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE Y 84 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N LYS Y 124 " --> pdb=" O PHE Y 84 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 6 through 15 removed outlier: 3.783A pdb=" N ARG Z 8 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'a' and resid 99 through 102 removed outlier: 3.676A pdb=" N SER a 101 " --> pdb=" O ILE a 108 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AF4, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.652A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG b 42 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 32 through 33 Processing sheet with id=AF6, first strand: chain 'e' and resid 30 through 31 removed outlier: 3.743A pdb=" N MET e 38 " --> pdb=" O ILE e 31 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'g' and resid 106 through 108 removed outlier: 3.689A pdb=" N SER g 115 " --> pdb=" O LYS g 107 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 139 through 140 removed outlier: 3.761A pdb=" N HIS g 139 " --> pdb=" O TYR g 148 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR g 148 " --> pdb=" O HIS g 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'h' and resid 5 through 11 removed outlier: 6.245A pdb=" N LEU h 7 " --> pdb=" O GLN h 311 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN h 311 " --> pdb=" O LEU h 7 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY h 9 " --> pdb=" O VAL h 309 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL h 307 " --> pdb=" O LEU h 11 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY h 301 " --> pdb=" O THR h 287 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 18 through 22 removed outlier: 6.652A pdb=" N ALA h 34 " --> pdb=" O THR h 19 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE h 21 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU h 32 " --> pdb=" O ILE h 21 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER h 33 " --> pdb=" O ILE h 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE h 41 " --> pdb=" O SER h 33 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 66 through 71 removed outlier: 3.636A pdb=" N ALA h 78 " --> pdb=" O TRP h 90 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG h 99 " --> pdb=" O LEU h 89 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP h 91 " --> pdb=" O THR h 97 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR h 97 " --> pdb=" O ASP h 91 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 108 through 113 removed outlier: 3.586A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE h 129 " --> pdb=" O THR h 141 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR h 141 " --> pdb=" O ILE h 129 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU h 131 " --> pdb=" O LYS h 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 151 through 155 Processing sheet with id=AG5, first strand: chain 'h' and resid 195 through 200 removed outlier: 3.654A pdb=" N THR h 197 " --> pdb=" O GLY h 210 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'h' and resid 239 through 241 removed outlier: 3.627A pdb=" N LEU h 248 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) 1454 hydrogen bonds defined for protein. 4122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1206 hydrogen bonds 2044 hydrogen bond angles 0 basepair planarities 477 basepair parallelities 878 stacking parallelities Total time for adding SS restraints: 63.59 Time building geometry restraints manager: 34.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 17358 1.34 - 1.46: 27996 1.46 - 1.58: 34773 1.58 - 1.70: 3704 1.70 - 1.82: 274 Bond restraints: 84105 Sorted by residual: bond pdb=" C ASP E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.19e-02 7.06e+03 4.56e+00 bond pdb=" C VAL a 62 " pdb=" N PRO a 63 " ideal model delta sigma weight residual 1.337 1.355 -0.019 9.80e-03 1.04e+04 3.59e+00 bond pdb=" CB PRO Y 62 " pdb=" CG PRO Y 62 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.03e+00 bond pdb=" CG PRO E 219 " pdb=" CD PRO E 219 " ideal model delta sigma weight residual 1.503 1.444 0.059 3.40e-02 8.65e+02 3.01e+00 bond pdb=" N PRO Y 62 " pdb=" CA PRO Y 62 " ideal model delta sigma weight residual 1.479 1.455 0.024 1.56e-02 4.11e+03 2.28e+00 ... (remaining 84100 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.40: 8316 104.40 - 111.81: 44127 111.81 - 119.23: 28446 119.23 - 126.65: 36170 126.65 - 134.07: 5390 Bond angle restraints: 122449 Sorted by residual: angle pdb=" CA PRO Y 62 " pdb=" N PRO Y 62 " pdb=" CD PRO Y 62 " ideal model delta sigma weight residual 112.00 103.40 8.60 1.40e+00 5.10e-01 3.77e+01 angle pdb=" CA PRO E 219 " pdb=" N PRO E 219 " pdb=" CD PRO E 219 " ideal model delta sigma weight residual 112.00 105.89 6.11 1.40e+00 5.10e-01 1.90e+01 angle pdb=" N PRO E 219 " pdb=" CD PRO E 219 " pdb=" CG PRO E 219 " ideal model delta sigma weight residual 103.20 96.98 6.22 1.50e+00 4.44e-01 1.72e+01 angle pdb=" C THR Z 50 " pdb=" N THR Z 51 " pdb=" CA THR Z 51 " ideal model delta sigma weight residual 120.67 125.97 -5.30 1.34e+00 5.57e-01 1.56e+01 angle pdb=" C3' U 2 688 " pdb=" O3' U 2 688 " pdb=" P U 2 689 " ideal model delta sigma weight residual 120.20 125.91 -5.71 1.50e+00 4.44e-01 1.45e+01 ... (remaining 122444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 45311 35.87 - 71.74: 1409 71.74 - 107.62: 129 107.62 - 143.49: 9 143.49 - 179.36: 28 Dihedral angle restraints: 46886 sinusoidal: 32830 harmonic: 14056 Sorted by residual: dihedral pdb=" O4' C 2 853 " pdb=" C1' C 2 853 " pdb=" N1 C 2 853 " pdb=" C2 C 2 853 " ideal model delta sinusoidal sigma weight residual -160.00 17.15 -177.15 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 10.70 -170.70 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual 200.00 36.43 163.57 1 1.50e+01 4.44e-03 8.36e+01 ... (remaining 46883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 14199 0.061 - 0.123: 947 0.123 - 0.184: 44 0.184 - 0.246: 3 0.246 - 0.307: 1 Chirality restraints: 15194 Sorted by residual: chirality pdb=" C1' U 21203 " pdb=" O4' U 21203 " pdb=" C2' U 21203 " pdb=" N1 U 21203 " both_signs ideal model delta sigma weight residual False 2.47 2.16 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1' A 2 531 " pdb=" O4' A 2 531 " pdb=" C2' A 2 531 " pdb=" N9 A 2 531 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C3' U z 160 " pdb=" C4' U z 160 " pdb=" O3' U z 160 " pdb=" C2' U z 160 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.19 2.00e-01 2.50e+01 9.46e-01 ... (remaining 15191 not shown) Planarity restraints: 8634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN Y 61 " -0.077 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO Y 62 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO Y 62 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO Y 62 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 218 " -0.057 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO E 219 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 219 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 219 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 23 " 0.049 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO C 24 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 24 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 24 " 0.041 5.00e-02 4.00e+02 ... (remaining 8631 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 3335 2.67 - 3.23: 68448 3.23 - 3.79: 138897 3.79 - 4.34: 182351 4.34 - 4.90: 263792 Nonbonded interactions: 656823 Sorted by model distance: nonbonded pdb=" O2' G 21550 " pdb=" O2 C 21558 " model vdw 2.115 2.440 nonbonded pdb=" OP2 C 2 98 " pdb=" O2' A 2 426 " model vdw 2.127 2.440 nonbonded pdb=" O2' A 21822 " pdb=" NZ LYS Y 60 " model vdw 2.154 2.520 nonbonded pdb=" OG SER B 2 " pdb=" OE1 GLU B 56 " model vdw 2.156 2.440 nonbonded pdb=" O2 U 2 372 " pdb=" O2' G 2 394 " model vdw 2.159 2.440 ... (remaining 656818 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 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: 0.060 Extract box with map and model: 18.930 Check model and map are aligned: 0.910 Set scattering table: 0.550 Process input model: 223.400 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.240 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: 0.030 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 252.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 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 : 0.002 0.087 84105 Z= 0.115 Angle : 0.495 10.371 122449 Z= 0.257 Chirality : 0.031 0.307 15194 Planarity : 0.004 0.112 8634 Dihedral : 15.178 179.362 37820 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.12), residues: 4821 helix: 1.35 (0.14), residues: 1484 sheet: -0.80 (0.19), residues: 767 loop : -1.69 (0.12), residues: 2570 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 756 time to evaluate : 4.689 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 756 average time/residue: 0.7453 time to fit residues: 968.7912 Evaluate side-chains 592 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 592 time to evaluate : 4.812 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 556 optimal weight: 5.9990 chunk 499 optimal weight: 0.9990 chunk 277 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 336 optimal weight: 5.9990 chunk 266 optimal weight: 7.9990 chunk 516 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 chunk 314 optimal weight: 3.9990 chunk 384 optimal weight: 5.9990 chunk 598 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 197 GLN I 25 GLN ** K 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 ASN ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN Y 63 ASN ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 26 GLN e 45 GLN f 88 GLN h 64 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 84105 Z= 0.220 Angle : 0.581 10.468 122449 Z= 0.287 Chirality : 0.035 0.263 15194 Planarity : 0.005 0.067 8634 Dihedral : 15.130 179.089 27708 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.12), residues: 4821 helix: 1.21 (0.14), residues: 1517 sheet: -0.78 (0.18), residues: 829 loop : -1.72 (0.12), residues: 2475 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 621 time to evaluate : 4.758 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 49 residues processed: 659 average time/residue: 0.7476 time to fit residues: 860.6475 Evaluate side-chains 616 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 567 time to evaluate : 4.682 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.5947 time to fit residues: 60.9946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 332 optimal weight: 30.0000 chunk 185 optimal weight: 9.9990 chunk 498 optimal weight: 10.0000 chunk 407 optimal weight: 30.0000 chunk 165 optimal weight: 20.0000 chunk 599 optimal weight: 8.9990 chunk 647 optimal weight: 30.0000 chunk 533 optimal weight: 10.0000 chunk 594 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 480 optimal weight: 30.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN C 101 HIS C 118 GLN C 157 GLN D 178 HIS ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 GLN J 181 GLN K 124 HIS ** K 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 HIS L 44 HIS N 75 ASN ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN V 92 HIS X 91 ASN ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 84 HIS ** h 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.090 84105 Z= 0.435 Angle : 0.835 13.998 122449 Z= 0.410 Chirality : 0.046 0.377 15194 Planarity : 0.007 0.064 8634 Dihedral : 16.131 179.680 27708 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.12), residues: 4821 helix: 0.11 (0.13), residues: 1527 sheet: -1.05 (0.17), residues: 837 loop : -2.18 (0.12), residues: 2457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 585 time to evaluate : 4.822 Fit side-chains revert: symmetry clash outliers start: 118 outliers final: 67 residues processed: 662 average time/residue: 0.7565 time to fit residues: 878.7113 Evaluate side-chains 612 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 545 time to evaluate : 4.779 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.6313 time to fit residues: 85.5204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 592 optimal weight: 4.9990 chunk 450 optimal weight: 0.0000 chunk 311 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 402 optimal weight: 3.9990 chunk 601 optimal weight: 0.0970 chunk 636 optimal weight: 0.0270 chunk 314 optimal weight: 10.0000 chunk 570 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 overall best weight: 1.8244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 84 HIS f 88 GLN h 14 HIS ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.067 84105 Z= 0.145 Angle : 0.557 9.661 122449 Z= 0.281 Chirality : 0.035 0.214 15194 Planarity : 0.004 0.061 8634 Dihedral : 15.547 179.362 27708 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 4821 helix: 0.85 (0.14), residues: 1524 sheet: -0.73 (0.18), residues: 821 loop : -1.91 (0.12), residues: 2476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 619 time to evaluate : 4.714 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 36 residues processed: 657 average time/residue: 0.7514 time to fit residues: 863.5182 Evaluate side-chains 607 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 571 time to evaluate : 4.770 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.6158 time to fit residues: 47.6296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 530 optimal weight: 7.9990 chunk 361 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 474 optimal weight: 0.0870 chunk 262 optimal weight: 6.9990 chunk 543 optimal weight: 6.9990 chunk 440 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 571 optimal weight: 3.9990 chunk 160 optimal weight: 40.0000 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 91 ASN ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 GLN Z 89 HIS ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN f 88 GLN h 64 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 84105 Z= 0.260 Angle : 0.627 11.315 122449 Z= 0.312 Chirality : 0.038 0.241 15194 Planarity : 0.005 0.063 8634 Dihedral : 15.680 179.832 27708 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4821 helix: 0.69 (0.13), residues: 1531 sheet: -0.84 (0.18), residues: 819 loop : -1.95 (0.12), residues: 2471 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 571 time to evaluate : 4.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 55 residues processed: 627 average time/residue: 0.7309 time to fit residues: 800.3481 Evaluate side-chains 602 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 547 time to evaluate : 4.703 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.5793 time to fit residues: 66.4959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 214 optimal weight: 4.9990 chunk 573 optimal weight: 6.9990 chunk 125 optimal weight: 30.0000 chunk 373 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 637 optimal weight: 0.3980 chunk 529 optimal weight: 8.9990 chunk 295 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS ** K 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 GLN ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN f 88 GLN ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 84105 Z= 0.202 Angle : 0.579 10.192 122449 Z= 0.290 Chirality : 0.036 0.212 15194 Planarity : 0.004 0.064 8634 Dihedral : 15.610 179.762 27708 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.12), residues: 4821 helix: 0.78 (0.13), residues: 1526 sheet: -0.84 (0.18), residues: 818 loop : -1.91 (0.12), residues: 2477 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 572 time to evaluate : 4.819 Fit side-chains revert: symmetry clash outliers start: 71 outliers final: 34 residues processed: 618 average time/residue: 0.7498 time to fit residues: 828.8475 Evaluate side-chains 589 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 555 time to evaluate : 4.787 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.5873 time to fit residues: 44.6403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 614 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 363 optimal weight: 2.9990 chunk 465 optimal weight: 9.9990 chunk 360 optimal weight: 3.9990 chunk 536 optimal weight: 4.9990 chunk 356 optimal weight: 10.0000 chunk 635 optimal weight: 10.0000 chunk 397 optimal weight: 7.9990 chunk 387 optimal weight: 4.9990 chunk 293 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 GLN ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN h 15 ASN h 215 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 84105 Z= 0.252 Angle : 0.629 13.323 122449 Z= 0.313 Chirality : 0.037 0.236 15194 Planarity : 0.005 0.064 8634 Dihedral : 15.736 179.664 27708 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.12), residues: 4821 helix: 0.63 (0.13), residues: 1527 sheet: -0.89 (0.18), residues: 820 loop : -1.96 (0.12), residues: 2474 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 560 time to evaluate : 4.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 37 residues processed: 609 average time/residue: 0.7405 time to fit residues: 786.4511 Evaluate side-chains 580 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 543 time to evaluate : 4.812 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.5994 time to fit residues: 48.6999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 392 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 379 optimal weight: 30.0000 chunk 191 optimal weight: 0.4980 chunk 124 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 403 optimal weight: 4.9990 chunk 432 optimal weight: 20.0000 chunk 314 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 499 optimal weight: 6.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** K 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 GLN ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN f 88 GLN h 15 ASN h 215 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 84105 Z= 0.227 Angle : 0.606 15.050 122449 Z= 0.303 Chirality : 0.037 0.218 15194 Planarity : 0.005 0.065 8634 Dihedral : 15.716 179.341 27708 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.12), residues: 4821 helix: 0.68 (0.13), residues: 1522 sheet: -0.86 (0.18), residues: 816 loop : -1.94 (0.12), residues: 2483 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 555 time to evaluate : 4.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 23 residues processed: 578 average time/residue: 0.7669 time to fit residues: 772.9228 Evaluate side-chains 559 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 536 time to evaluate : 4.684 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5750 time to fit residues: 31.0669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 577 optimal weight: 1.9990 chunk 608 optimal weight: 0.2980 chunk 555 optimal weight: 6.9990 chunk 591 optimal weight: 5.9990 chunk 356 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 chunk 464 optimal weight: 0.2980 chunk 181 optimal weight: 7.9990 chunk 534 optimal weight: 0.9990 chunk 559 optimal weight: 3.9990 chunk 589 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 127 ASN ** W 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 GLN Y 23 HIS ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN e 37 ASN h 14 HIS h 215 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.082 84105 Z= 0.132 Angle : 0.533 12.966 122449 Z= 0.268 Chirality : 0.034 0.211 15194 Planarity : 0.004 0.063 8634 Dihedral : 15.429 179.157 27708 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.12), residues: 4821 helix: 1.01 (0.14), residues: 1503 sheet: -0.76 (0.18), residues: 807 loop : -1.76 (0.12), residues: 2511 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 595 time to evaluate : 4.776 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 6 residues processed: 607 average time/residue: 0.7708 time to fit residues: 828.2945 Evaluate side-chains 570 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 564 time to evaluate : 4.731 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5881 time to fit residues: 12.2866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 388 optimal weight: 20.0000 chunk 625 optimal weight: 20.0000 chunk 382 optimal weight: 1.9990 chunk 296 optimal weight: 0.7980 chunk 435 optimal weight: 2.9990 chunk 656 optimal weight: 20.0000 chunk 604 optimal weight: 0.0980 chunk 522 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 403 optimal weight: 20.0000 chunk 320 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 84105 Z= 0.167 Angle : 0.549 13.395 122449 Z= 0.274 Chirality : 0.034 0.216 15194 Planarity : 0.004 0.069 8634 Dihedral : 15.424 179.301 27708 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.12), residues: 4821 helix: 0.99 (0.14), residues: 1506 sheet: -0.74 (0.18), residues: 807 loop : -1.74 (0.12), residues: 2508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 565 time to evaluate : 4.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 577 average time/residue: 0.7508 time to fit residues: 756.4676 Evaluate side-chains 566 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 556 time to evaluate : 4.747 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5949 time to fit residues: 17.2318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 415 optimal weight: 0.2980 chunk 556 optimal weight: 2.9990 chunk 160 optimal weight: 30.0000 chunk 482 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 145 optimal weight: 30.0000 chunk 523 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 537 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 overall best weight: 5.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN K 27 GLN ** K 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 105 ASN V 81 GLN ** W 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN d 26 GLN ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN h 215 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.097831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.076892 restraints weight = 253438.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.076591 restraints weight = 186912.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.077110 restraints weight = 156262.381| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.103 84105 Z= 0.287 Angle : 0.665 15.293 122449 Z= 0.330 Chirality : 0.039 0.229 15194 Planarity : 0.005 0.067 8634 Dihedral : 15.788 179.634 27708 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.12), residues: 4821 helix: 0.59 (0.13), residues: 1519 sheet: -0.84 (0.18), residues: 786 loop : -1.91 (0.12), residues: 2516 =============================================================================== Job complete usr+sys time: 13477.14 seconds wall clock time: 241 minutes 27.13 seconds (14487.13 seconds total)