Starting phenix.real_space_refine (version: dev) on Thu Dec 15 12:25:34 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syj_25530/12_2022/7syj_25530.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syj_25530/12_2022/7syj_25530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syj_25530/12_2022/7syj_25530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syj_25530/12_2022/7syj_25530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syj_25530/12_2022/7syj_25530.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syj_25530/12_2022/7syj_25530.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B GLU 56": "OE1" <-> "OE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 162": "OD1" <-> "OD2" Residue "F PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "H ASP 20": "OD1" <-> "OD2" Residue "H GLU 219": "OE1" <-> "OE2" Residue "I ASP 35": "OD1" <-> "OD2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "L TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 103": "OE1" <-> "OE2" Residue "O GLU 35": "OE1" <-> "OE2" Residue "O PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 67": "OD1" <-> "OD2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 36": "OE1" <-> "OE2" Residue "S TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X GLU 87": "OE1" <-> "OE2" Residue "b GLU 46": "OE1" <-> "OE2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 68": "OD1" <-> "OD2" Residue "h PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 223": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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': 114, 'rna3p_pur': 754, 'rna3p_pyr': 686} Link IDs: {'rna2p': 256, 'rna3p': 1440} 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: "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': 15, 'rna3p_pur': 73, 'rna3p_pyr': 63} Link IDs: {'rna2p': 25, 'rna3p': 136} Chain breaks: 1 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: "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 93.632 130.162 134.754 1.00 62.36 S ATOM 69352 SG CYS b 26 96.510 130.374 137.381 1.00 61.53 S ATOM 69735 SG CYS b 74 95.879 127.819 136.001 1.00 63.87 S ATOM 69754 SG CYS b 77 93.113 129.845 138.485 1.00 67.13 S ATOM 71745 SG CYS g 121 151.070 97.146 239.991 1.00380.14 S ATOM 71781 SG CYS g 126 148.244 96.855 240.063 1.00381.77 S ATOM 71899 SG CYS g 141 150.282 99.040 237.580 1.00396.98 S ATOM 71918 SG CYS g 144 147.351 99.419 239.872 1.00390.32 S Time building chain proxies: 32.98, per 1000 atoms: 0.42 Number of scatterers: 78761 At special positions: 0 Unit cell: (234.65, 193.8, 259.35, 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: 31.54 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " 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: 136 helices and 55 sheets defined 32.6% alpha, 15.7% beta 478 base pairs and 924 stacking pairs defined. Time for finding SS restraints: 22.95 Creating SS restraints... Processing helix chain 'B' and resid 12 through 22 removed outlier: 4.007A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 67 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 84 through 94 removed outlier: 3.631A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 167 through 187 Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.887A pdb=" N ILE B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 removed outlier: 4.078A pdb=" N SER C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.674A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 178 removed outlier: 3.917A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.703A pdb=" N HIS C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.699A pdb=" N ARG D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.506A 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 246 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.919A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 removed outlier: 5.476A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.088A 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 54 through 59 removed outlier: 3.715A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.839A pdb=" N LEU E 96 " --> pdb=" O THR E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 97 through 111 removed outlier: 4.247A pdb=" N GLY E 111 " --> pdb=" O TYR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 130 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'F' and resid 15 through 19 removed outlier: 3.525A pdb=" N TRP F 18 " --> pdb=" O PRO F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 59 through 67 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 removed outlier: 3.508A pdb=" N GLY F 263 " --> pdb=" O LYS F 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 76 removed outlier: 3.655A pdb=" N THR G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 105 removed outlier: 3.932A pdb=" N HIS G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR G 104 " --> pdb=" O ILE G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.678A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU G 112 " --> pdb=" O PRO G 108 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN G 118 " --> pdb=" O ASN G 114 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER G 119 " --> pdb=" O ALA G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.698A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 201 Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 237 removed outlier: 3.657A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 34 Processing helix chain 'I' and resid 68 through 73 removed outlier: 3.790A pdb=" N PHE I 72 " --> pdb=" O GLN I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 87 Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.224A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.784A pdb=" N GLU I 167 " --> pdb=" O ASN I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 88 through 92 Processing helix chain 'J' and resid 106 through 117 Processing helix chain 'J' and resid 134 through 139 Processing helix chain 'J' and resid 143 through 155 removed outlier: 3.929A pdb=" N ASN J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 192 through 207 removed outlier: 3.541A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.486A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 95 through 100 removed outlier: 3.582A pdb=" N LEU K 98 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU K 100 " --> pdb=" O ILE K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 108 removed outlier: 3.603A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG K 108 " --> pdb=" O ASP K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 163 through 167 Processing helix chain 'K' and resid 171 through 185 removed outlier: 3.976A pdb=" N ARG K 175 " --> pdb=" O GLY K 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.803A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 removed outlier: 3.829A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'M' and resid 47 through 52 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 Processing helix chain 'N' and resid 120 through 130 removed outlier: 3.683A pdb=" N CYS N 130 " --> pdb=" O GLU N 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 43 Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 70 through 79 removed outlier: 3.523A pdb=" N ILE O 74 " --> pdb=" O LYS O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 105 removed outlier: 3.930A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 132 Processing helix chain 'P' and resid 64 through 68 removed outlier: 3.619A pdb=" N ASP P 67 " --> pdb=" O ALA P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 110 through 123 removed outlier: 3.570A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY P 123 " --> pdb=" O LEU P 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.579A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'Q' and resid 86 through 90 removed outlier: 3.858A pdb=" N VAL Q 90 " --> pdb=" O PRO Q 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 52 Processing helix chain 'R' and resid 52 through 59 Processing helix chain 'R' and resid 77 through 99 removed outlier: 3.852A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.618A 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 removed outlier: 3.807A pdb=" N LYS S 10 " --> pdb=" O THR S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 39 Processing helix chain 'S' and resid 44 through 64 Processing helix chain 'S' and resid 78 through 82 removed outlier: 3.519A pdb=" N ASP S 82 " --> pdb=" O GLU S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 107 Processing helix chain 'T' and resid 28 through 33 removed outlier: 3.693A pdb=" N ILE T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 45 removed outlier: 3.844A pdb=" N ALA T 41 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 removed outlier: 3.799A pdb=" N VAL T 64 " --> pdb=" O THR T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.679A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 117 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 12 through 26 removed outlier: 4.456A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 73 through 79 removed outlier: 3.636A pdb=" N LYS U 77 " --> pdb=" O GLY U 73 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE U 78 " --> pdb=" O SER U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 110 Processing helix chain 'U' and resid 124 through 143 Processing helix chain 'V' and resid 29 through 46 Processing helix chain 'V' and resid 94 through 103 Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.932A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 77 Processing helix chain 'X' and resid 5 through 21 removed outlier: 3.514A pdb=" N ASP X 9 " --> pdb=" O ASN X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 45 Processing helix chain 'X' and resid 85 through 94 Processing helix chain 'X' and resid 113 through 120 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 27 through 31 removed outlier: 3.505A pdb=" N HIS Y 31 " --> pdb=" O LYS Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 38 removed outlier: 3.879A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 93 removed outlier: 4.114A pdb=" N ASN Y 92 " --> pdb=" O GLY Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 49 removed outlier: 3.692A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 removed outlier: 3.715A pdb=" N ASN Z 85 " --> pdb=" O TYR Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 95 removed outlier: 3.792A 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 126 removed outlier: 4.135A pdb=" N ASN Z 124 " --> pdb=" O THR Z 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 65 Proline residue: a 63 - end of helix Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 95 removed outlier: 3.521A pdb=" N ALA a 84 " --> pdb=" O ARG a 80 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY a 95 " --> pdb=" O LEU a 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 56 Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 32 through 36 removed outlier: 4.283A pdb=" N GLY e 35 " --> pdb=" O ARG e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 46 Processing helix chain 'f' and resid 105 through 115 Processing helix chain 'g' and resid 101 through 105 Processing helix chain 'n' and resid 3 through 24 Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.711A pdb=" N GLU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.106A 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: 3.687A pdb=" N LEU B 147 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.545A pdb=" N GLY C 102 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 13.170A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.315A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 137 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 123 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.545A pdb=" N GLY C 102 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 13.170A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.315A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE C 142 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 104 through 113 removed outlier: 6.795A pdb=" N PHE D 127 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE D 109 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS D 125 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG D 123 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 128 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY D 140 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY D 138 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 185 through 188 Processing sheet with id=AA8, first strand: chain 'E' and resid 46 through 48 removed outlier: 3.925A pdb=" N GLU E 85 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE E 48 " --> pdb=" O GLU E 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 51 through 52 removed outlier: 3.534A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 150 through 155 removed outlier: 3.609A pdb=" N MET E 150 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 4.097A 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: 3.952A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG E 173 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 186 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 224 through 226 removed outlier: 4.171A pdb=" N GLU E 225 " --> pdb=" O ASN h 187 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN h 187 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 9 through 10 removed outlier: 4.301A pdb=" N LEU F 9 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 76 removed outlier: 4.263A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.722A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA F 110 " --> pdb=" O ILE F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 147 through 148 removed outlier: 6.321A pdb=" N HIS F 138 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE F 129 " --> pdb=" O HIS F 138 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL F 140 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR F 159 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE F 172 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN F 161 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 179 through 181 removed outlier: 6.604A pdb=" N LEU F 180 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS F 230 " --> pdb=" O LYS F 233 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 193 through 199 removed outlier: 6.792A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 123 through 124 removed outlier: 3.518A pdb=" N LYS d 47 " --> pdb=" O ASP G 140 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG d 44 " --> pdb=" O VAL d 30 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL d 30 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N CYS d 27 " --> pdb=" O ARG d 20 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG d 20 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN d 29 " --> pdb=" O LEU d 18 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS d 16 " --> pdb=" O ARG d 31 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU d 33 " --> pdb=" O VAL d 14 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL d 14 " --> pdb=" O GLU d 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 12 through 17 removed outlier: 4.099A pdb=" N GLY H 54 " --> pdb=" O ASN H 110 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL H 112 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE H 52 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL H 114 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL H 50 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.716A pdb=" N LEU H 75 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 160 through 162 removed outlier: 4.056A pdb=" N LYS H 160 " --> pdb=" O LYS H 172 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS H 172 " --> pdb=" O LYS H 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 47 through 51 removed outlier: 3.519A pdb=" N ILE I 95 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 184 through 187 removed outlier: 4.545A pdb=" N ASP I 184 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE X 52 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS X 60 " --> pdb=" O ILE X 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL X 63 " --> pdb=" O VAL X 25 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.949A pdb=" N ILE J 3 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 37 through 38 removed outlier: 3.618A pdb=" N LEU J 60 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS J 54 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL J 46 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU J 58 " --> pdb=" O ARG J 42 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 62 through 64 removed outlier: 7.974A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE J 101 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 140 through 141 Processing sheet with id=AD2, first strand: chain 'L' and resid 20 through 21 removed outlier: 3.826A pdb=" N MET L 21 " --> pdb=" O TRP L 69 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP L 69 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR L 68 " --> pdb=" O GLN L 61 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN L 61 " --> pdb=" O TYR L 68 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 72 through 79 removed outlier: 17.452A pdb=" N ILE M 72 " --> pdb=" O LEU M 93 " (cutoff:3.500A) removed outlier: 14.701A pdb=" N LEU M 93 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N SER M 74 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP M 91 " --> pdb=" O SER M 74 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG M 90 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N PHE M 140 " --> pdb=" O ASN M 108 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N SER M 110 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N VAL M 142 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS M 112 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N LYS M 144 " --> pdb=" O HIS M 112 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 49 through 53 removed outlier: 4.337A pdb=" N CYS N 50 " --> pdb=" O ASN N 75 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE N 77 " --> pdb=" O CYS N 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 52 through 57 removed outlier: 3.733A pdb=" N CYS P 54 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL P 30 " --> pdb=" O THR P 45 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 52 through 57 removed outlier: 3.733A pdb=" N CYS P 54 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL P 30 " --> pdb=" O THR P 45 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 94 through 96 removed outlier: 3.628A pdb=" N VAL Q 94 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 11 through 13 removed outlier: 7.249A pdb=" N LYS R 33 " --> pdb=" O VAL R 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 96 through 98 removed outlier: 5.627A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'U' and resid 81 through 82 Processing sheet with id=AE2, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.821A pdb=" N VAL V 54 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU V 88 " --> pdb=" O VAL V 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE V 22 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR V 25 " --> pdb=" O GLU V 111 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.821A pdb=" N VAL V 54 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU V 88 " --> pdb=" O VAL V 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE V 22 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG V 21 " --> pdb=" O THR V 115 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR V 115 " --> pdb=" O ARG V 21 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 62 through 65 Processing sheet with id=AE5, first strand: chain 'W' and resid 35 through 36 Processing sheet with id=AE6, first strand: chain 'X' and resid 109 through 112 removed outlier: 7.277A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU X 126 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 80 through 82 removed outlier: 5.606A pdb=" N ARG Y 67 " --> pdb=" O GLY Y 56 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY Y 56 " --> pdb=" O ARG Y 67 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS Y 69 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LYS Y 54 " --> pdb=" O CYS Y 69 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU Y 52 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS Y 124 " --> pdb=" O LEU Y 101 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA Y 103 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL Y 122 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 6 through 15 removed outlier: 6.695A pdb=" N ILE Z 7 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU Z 28 " --> pdb=" O ILE Z 7 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR Z 9 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP Z 26 " --> pdb=" O THR Z 9 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS Z 11 " --> pdb=" O VAL Z 24 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL Z 24 " --> pdb=" O LYS Z 11 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET Z 23 " --> pdb=" O GLY Z 73 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL Z 27 " --> pdb=" O THR Z 69 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR Z 69 " --> pdb=" O VAL Z 27 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS Z 68 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR Z 62 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.574A pdb=" N LEU b 71 " --> pdb=" O LYS b 38 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG b 42 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'g' and resid 133 through 134 removed outlier: 3.581A pdb=" N TYR g 140 " --> pdb=" O ALA g 133 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'h' and resid 5 through 11 removed outlier: 5.289A pdb=" N LEU h 7 " --> pdb=" O GLN h 311 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN h 311 " --> pdb=" O LEU h 7 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY h 9 " --> pdb=" O VAL h 309 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL h 309 " --> pdb=" O GLY h 9 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLY h 301 " --> pdb=" O THR h 287 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'h' and resid 18 through 22 removed outlier: 4.462A pdb=" N MET h 42 " --> pdb=" O ARG h 57 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG h 57 " --> pdb=" O MET h 42 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'h' and resid 66 through 71 removed outlier: 3.558A pdb=" N ARG h 88 " --> pdb=" O SER h 80 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU h 87 " --> pdb=" O ARG h 100 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ARG h 100 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU h 89 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'h' and resid 108 through 112 removed outlier: 3.603A pdb=" N SER h 122 " --> pdb=" O LYS h 130 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE h 129 " --> pdb=" O THR h 141 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR h 141 " --> pdb=" O ILE h 129 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU h 131 " --> pdb=" O LYS h 139 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 151 through 156 Processing sheet with id=AF7, first strand: chain 'h' and resid 195 through 199 removed outlier: 3.569A pdb=" N SER h 209 " --> pdb=" O MET h 217 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET h 217 " --> pdb=" O SER h 209 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU h 230 " --> pdb=" O ALA h 216 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR h 228 " --> pdb=" O LEU h 218 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.630A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU h 248 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP h 259 " --> pdb=" O LEU h 248 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE h 256 " --> pdb=" O GLU h 269 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU h 269 " --> pdb=" O ILE h 256 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE h 258 " --> pdb=" O VAL h 267 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 44 through 47 removed outlier: 3.753A pdb=" N THR c 44 " --> pdb=" O VAL c 35 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP c 34 " --> pdb=" O ARG c 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 64 through 65 removed outlier: 3.777A pdb=" N ARG c 72 " --> pdb=" O GLN c 65 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1206 hydrogen bonds 2026 hydrogen bond angles 0 basepair planarities 478 basepair parallelities 924 stacking parallelities Total time for adding SS restraints: 64.69 Time building geometry restraints manager: 34.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 17491 1.34 - 1.46: 29999 1.46 - 1.58: 32637 1.58 - 1.71: 3704 1.71 - 1.83: 274 Bond restraints: 84105 Sorted by residual: bond pdb=" C ASP E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.08e-02 8.57e+03 2.59e+01 bond pdb=" CA THR F 184 " pdb=" CB THR F 184 " ideal model delta sigma weight residual 1.531 1.617 -0.086 3.28e-02 9.30e+02 6.88e+00 bond pdb=" C3' G 2 752 " pdb=" O3' G 2 752 " ideal model delta sigma weight residual 1.427 1.456 -0.029 1.50e-02 4.44e+03 3.84e+00 bond pdb=" C3' U 2 553 " pdb=" O3' U 2 553 " ideal model delta sigma weight residual 1.427 1.455 -0.028 1.50e-02 4.44e+03 3.48e+00 bond pdb=" CB ASP C 90 " pdb=" CG ASP C 90 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.24e+00 ... (remaining 84100 not shown) Histogram of bond angle deviations from ideal: 96.59 - 104.29: 7643 104.29 - 111.98: 44767 111.98 - 119.68: 32662 119.68 - 127.38: 33399 127.38 - 135.08: 3978 Bond angle restraints: 122449 Sorted by residual: angle pdb=" N VAL D 63 " pdb=" CA VAL D 63 " pdb=" C VAL D 63 " ideal model delta sigma weight residual 113.53 107.49 6.04 9.80e-01 1.04e+00 3.80e+01 angle pdb=" CG ARG J 141 " pdb=" CD ARG J 141 " pdb=" NE ARG J 141 " ideal model delta sigma weight residual 112.00 124.32 -12.32 2.20e+00 2.07e-01 3.14e+01 angle pdb=" C PRO E 43 " pdb=" N THR E 44 " pdb=" CA THR E 44 " ideal model delta sigma weight residual 121.54 132.17 -10.63 1.91e+00 2.74e-01 3.10e+01 angle pdb=" C3' A z 252 " pdb=" O3' A z 252 " pdb=" P G z 253 " ideal model delta sigma weight residual 120.20 127.89 -7.69 1.50e+00 4.44e-01 2.63e+01 angle pdb=" N ILE E 198 " pdb=" CA ILE E 198 " pdb=" C ILE E 198 " ideal model delta sigma weight residual 113.47 108.42 5.05 1.01e+00 9.80e-01 2.50e+01 ... (remaining 122444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 45322 35.99 - 71.99: 1414 71.99 - 107.98: 116 107.98 - 143.97: 5 143.97 - 179.97: 29 Dihedral angle restraints: 46886 sinusoidal: 32830 harmonic: 14056 Sorted by residual: dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual -160.00 7.89 -167.89 1 1.50e+01 4.44e-03 8.44e+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 0.43 -160.43 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" O4' U 21624 " pdb=" C1' U 21624 " pdb=" N1 U 21624 " pdb=" C2 U 21624 " ideal model delta sinusoidal sigma weight residual -160.00 -2.01 -157.99 1 1.50e+01 4.44e-03 8.22e+01 ... (remaining 46883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 14371 0.087 - 0.174: 769 0.174 - 0.261: 40 0.261 - 0.348: 12 0.348 - 0.435: 2 Chirality restraints: 15194 Sorted by residual: chirality pdb=" CB ILE Q 85 " pdb=" CA ILE Q 85 " pdb=" CG1 ILE Q 85 " pdb=" CG2 ILE Q 85 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB ILE M 72 " pdb=" CA ILE M 72 " pdb=" CG1 ILE M 72 " pdb=" CG2 ILE M 72 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB VAL B 66 " pdb=" CA VAL B 66 " pdb=" CG1 VAL B 66 " pdb=" CG2 VAL B 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 15191 not shown) Planarity restraints: 8634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER M 114 " 0.088 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO M 115 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO M 115 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO M 115 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 212 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO E 213 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO E 213 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO E 213 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP U 33 " 0.019 2.00e-02 2.50e+03 1.96e-02 9.61e+00 pdb=" CG TRP U 33 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP U 33 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP U 33 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP U 33 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP U 33 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP U 33 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP U 33 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP U 33 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP U 33 " 0.003 2.00e-02 2.50e+03 ... (remaining 8631 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 13966 2.77 - 3.30: 65295 3.30 - 3.84: 149520 3.84 - 4.37: 167716 4.37 - 4.90: 249416 Nonbonded interactions: 645913 Sorted by model distance: nonbonded pdb=" O2 U z 144 " pdb=" O6 G z 249 " model vdw 2.240 3.040 nonbonded pdb=" O2 U z 262 " pdb=" O6 G z 271 " model vdw 2.248 2.432 nonbonded pdb=" O2' U 2 571 " pdb=" O PHE Z 60 " model vdw 2.265 2.440 nonbonded pdb=" OG1 THR B 144 " pdb=" O TYR B 156 " model vdw 2.267 2.440 nonbonded pdb=" OP2 C 2 98 " pdb=" O2' A 2 426 " model vdw 2.275 2.440 ... (remaining 645908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 18.480 Check model and map are aligned: 0.880 Convert atoms to be neutral: 0.520 Process input model: 224.030 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 251.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 84105 Z= 0.194 Angle : 0.789 13.850 122449 Z= 0.386 Chirality : 0.040 0.435 15194 Planarity : 0.006 0.133 8634 Dihedral : 15.073 179.965 37820 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer Outliers : 0.02 % 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: -2.97 (0.10), residues: 4821 helix: -1.68 (0.11), residues: 1453 sheet: -1.44 (0.19), residues: 755 loop : -2.34 (0.10), residues: 2613 *********************** 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 867 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 866 time to evaluate : 4.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 867 average time/residue: 0.7890 time to fit residues: 1124.2128 Evaluate side-chains 392 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 4.512 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4550 ------------------------------------------------------------------------------- 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: 20.0000 chunk 499 optimal weight: 5.9990 chunk 277 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 336 optimal weight: 0.9990 chunk 266 optimal weight: 7.9990 chunk 516 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 314 optimal weight: 20.0000 chunk 384 optimal weight: 20.0000 chunk 598 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS B 193 HIS ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 8 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN G 118 ASN H 187 HIS J 87 ASN ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS U 83 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN Y 110 HIS Z 94 HIS ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 285 GLN ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 84105 Z= 0.209 Angle : 0.605 9.538 122449 Z= 0.308 Chirality : 0.036 0.498 15194 Planarity : 0.005 0.076 8634 Dihedral : 15.381 179.968 27708 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.19 % 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: -2.02 (0.11), residues: 4821 helix: -0.16 (0.13), residues: 1481 sheet: -1.48 (0.19), residues: 790 loop : -2.05 (0.11), residues: 2550 *********************** 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 512 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 504 time to evaluate : 4.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 510 average time/residue: 0.7176 time to fit residues: 630.3535 Evaluate side-chains 341 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 340 time to evaluate : 4.605 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5286 time to fit residues: 6.5358 ------------------------------------------------------------------------------- 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: 5.9990 chunk 185 optimal weight: 6.9990 chunk 498 optimal weight: 20.0000 chunk 407 optimal weight: 8.9990 chunk 165 optimal weight: 30.0000 chunk 599 optimal weight: 9.9990 chunk 647 optimal weight: 40.0000 chunk 533 optimal weight: 9.9990 chunk 594 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 480 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN E 226 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN J 167 GLN K 132 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 GLN T 10 GLN U 12 GLN X 44 HIS ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 GLN ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.104 84105 Z= 0.211 Angle : 0.617 12.656 122449 Z= 0.310 Chirality : 0.036 0.228 15194 Planarity : 0.005 0.108 8634 Dihedral : 15.591 179.776 27708 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.43 % Favored : 93.55 % Rotamer Outliers : 0.31 % 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: -1.71 (0.12), residues: 4821 helix: 0.17 (0.13), residues: 1495 sheet: -1.25 (0.19), residues: 759 loop : -1.93 (0.12), residues: 2567 *********************** 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 484 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 471 time to evaluate : 4.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 483 average time/residue: 0.7301 time to fit residues: 604.4664 Evaluate side-chains 345 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 339 time to evaluate : 4.634 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5390 time to fit residues: 11.7245 ------------------------------------------------------------------------------- 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: 5.9990 chunk 450 optimal weight: 8.9990 chunk 311 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 286 optimal weight: 0.5980 chunk 402 optimal weight: 5.9990 chunk 601 optimal weight: 5.9990 chunk 636 optimal weight: 30.0000 chunk 314 optimal weight: 0.5980 chunk 570 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 84 GLN B 193 HIS ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 HIS J 167 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS O 101 HIS ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.104 84105 Z= 0.150 Angle : 0.528 9.121 122449 Z= 0.267 Chirality : 0.033 0.247 15194 Planarity : 0.004 0.053 8634 Dihedral : 15.442 179.255 27708 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.05 % 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: -1.43 (0.12), residues: 4821 helix: 0.58 (0.14), residues: 1490 sheet: -1.27 (0.19), residues: 769 loop : -1.82 (0.12), residues: 2562 *********************** 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 470 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 468 time to evaluate : 5.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 470 average time/residue: 0.7418 time to fit residues: 600.1389 Evaluate side-chains 331 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 4.534 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4940 ------------------------------------------------------------------------------- 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: 8.9990 chunk 361 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 474 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 543 optimal weight: 8.9990 chunk 440 optimal weight: 0.0060 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 5.9990 chunk 571 optimal weight: 6.9990 chunk 160 optimal weight: 30.0000 overall best weight: 5.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 50 ASN B 84 GLN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 267 GLN E 22 ASN E 57 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN J 167 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS X 44 HIS X 91 ASN ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 84105 Z= 0.208 Angle : 0.589 9.917 122449 Z= 0.299 Chirality : 0.035 0.229 15194 Planarity : 0.005 0.049 8634 Dihedral : 15.651 179.865 27708 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 0.14 % 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: -1.41 (0.12), residues: 4821 helix: 0.62 (0.14), residues: 1472 sheet: -1.35 (0.18), residues: 776 loop : -1.78 (0.12), residues: 2573 *********************** 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 452 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 446 time to evaluate : 4.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 450 average time/residue: 0.7251 time to fit residues: 566.3544 Evaluate side-chains 326 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 4.564 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4923 ------------------------------------------------------------------------------- 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: 20.0000 chunk 125 optimal weight: 40.0000 chunk 373 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 637 optimal weight: 30.0000 chunk 529 optimal weight: 20.0000 chunk 295 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 0.9990 chunk 334 optimal weight: 7.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 36 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN E 57 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 HIS ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS T 87 GLN ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 84 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.097 84105 Z= 0.280 Angle : 0.698 11.424 122449 Z= 0.354 Chirality : 0.039 0.242 15194 Planarity : 0.006 0.075 8634 Dihedral : 16.170 179.529 27708 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer Outliers : 0.09 % 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: -1.76 (0.12), residues: 4821 helix: 0.27 (0.13), residues: 1462 sheet: -1.55 (0.19), residues: 712 loop : -1.95 (0.11), residues: 2647 *********************** 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 427 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 423 time to evaluate : 4.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 425 average time/residue: 0.7462 time to fit residues: 547.1473 Evaluate side-chains 309 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 4.583 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4950 ------------------------------------------------------------------------------- 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: 8.9990 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 1.9990 chunk 465 optimal weight: 2.9990 chunk 360 optimal weight: 2.9990 chunk 536 optimal weight: 5.9990 chunk 356 optimal weight: 7.9990 chunk 635 optimal weight: 40.0000 chunk 397 optimal weight: 9.9990 chunk 387 optimal weight: 0.0070 chunk 293 optimal weight: 9.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 84 GLN B 193 HIS ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 GLN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 3 HIS ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.063 84105 Z= 0.145 Angle : 0.552 10.036 122449 Z= 0.281 Chirality : 0.034 0.226 15194 Planarity : 0.004 0.077 8634 Dihedral : 15.800 179.950 27708 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.05 % 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: -1.40 (0.12), residues: 4821 helix: 0.66 (0.14), residues: 1469 sheet: -1.45 (0.18), residues: 772 loop : -1.76 (0.12), residues: 2580 *********************** 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 454 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 452 time to evaluate : 4.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 453 average time/residue: 0.7456 time to fit residues: 583.4330 Evaluate side-chains 333 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 4.556 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4979 ------------------------------------------------------------------------------- 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: 6.9990 chunk 253 optimal weight: 8.9990 chunk 379 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 124 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 403 optimal weight: 6.9990 chunk 432 optimal weight: 10.0000 chunk 314 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 499 optimal weight: 0.4980 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 84105 Z= 0.225 Angle : 0.621 9.625 122449 Z= 0.315 Chirality : 0.037 0.303 15194 Planarity : 0.005 0.056 8634 Dihedral : 15.994 179.611 27708 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % 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: -1.54 (0.12), residues: 4821 helix: 0.52 (0.14), residues: 1477 sheet: -1.54 (0.19), residues: 742 loop : -1.83 (0.12), residues: 2602 *********************** 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 410 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 4.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.7257 time to fit residues: 515.9685 Evaluate side-chains 321 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 4.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5275 ------------------------------------------------------------------------------- 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: 5.9990 chunk 608 optimal weight: 9.9990 chunk 555 optimal weight: 9.9990 chunk 591 optimal weight: 20.0000 chunk 356 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 464 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 534 optimal weight: 0.9980 chunk 559 optimal weight: 6.9990 chunk 589 optimal weight: 9.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 HIS ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 ASN ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 84105 Z= 0.225 Angle : 0.632 9.773 122449 Z= 0.321 Chirality : 0.037 0.257 15194 Planarity : 0.005 0.058 8634 Dihedral : 16.144 179.640 27708 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer Outliers : 0.02 % 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: -1.63 (0.12), residues: 4821 helix: 0.38 (0.13), residues: 1485 sheet: -1.55 (0.19), residues: 735 loop : -1.86 (0.12), residues: 2601 *********************** 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 425 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 424 time to evaluate : 4.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 425 average time/residue: 0.7773 time to fit residues: 570.5406 Evaluate side-chains 319 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 4.632 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0432 ------------------------------------------------------------------------------- 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: 10.0000 chunk 625 optimal weight: 6.9990 chunk 382 optimal weight: 0.0770 chunk 296 optimal weight: 1.9990 chunk 435 optimal weight: 0.7980 chunk 656 optimal weight: 9.9990 chunk 604 optimal weight: 0.6980 chunk 522 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 403 optimal weight: 20.0000 chunk 320 optimal weight: 3.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN C 76 ASN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS U 85 ASN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 127 ASN ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 106 GLN a 112 ASN ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 84105 Z= 0.133 Angle : 0.554 10.050 122449 Z= 0.282 Chirality : 0.034 0.295 15194 Planarity : 0.004 0.056 8634 Dihedral : 15.854 179.297 27708 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.09 % 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: -1.45 (0.12), residues: 4821 helix: 0.60 (0.14), residues: 1486 sheet: -1.56 (0.19), residues: 761 loop : -1.75 (0.12), residues: 2574 ********************** 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 437 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 433 time to evaluate : 4.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 437 average time/residue: 0.7229 time to fit residues: 547.7208 Evaluate side-chains 343 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 342 time to evaluate : 4.570 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5482 time to fit residues: 6.6202 ------------------------------------------------------------------------------- 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: 8.9990 chunk 556 optimal weight: 9.9990 chunk 160 optimal weight: 30.0000 chunk 482 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 40.0000 chunk 523 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 537 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN E 22 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 127 ASN ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 ASN ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 28 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.055012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.044385 restraints weight = 820635.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.044839 restraints weight = 529372.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.045140 restraints weight = 346710.685| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 84105 Z= 0.283 Angle : 0.701 10.093 122449 Z= 0.354 Chirality : 0.040 0.307 15194 Planarity : 0.005 0.058 8634 Dihedral : 16.297 178.916 27708 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.35 % Favored : 90.62 % Rotamer Outliers : 0.02 % 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: -1.73 (0.12), residues: 4821 helix: 0.29 (0.13), residues: 1481 sheet: -1.57 (0.19), residues: 723 loop : -1.92 (0.12), residues: 2617 =============================================================================== Job complete usr+sys time: 10973.50 seconds wall clock time: 198 minutes 50.53 seconds (11930.53 seconds total)