Starting phenix.real_space_refine (version: dev) on Thu Dec 15 12:00:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syl_25532/12_2022/7syl_25532.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syl_25532/12_2022/7syl_25532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syl_25532/12_2022/7syl_25532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syl_25532/12_2022/7syl_25532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syl_25532/12_2022/7syl_25532.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syl_25532/12_2022/7syl_25532.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 271": "OD1" <-> "OD2" Residue "E PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "I GLU 18": "OE1" <-> "OE2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K ASP 152": "OD1" <-> "OD2" Residue "L TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L ASP 26": "OD1" <-> "OD2" Residue "L TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 31": "OE1" <-> "OE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M GLU 103": "OE1" <-> "OE2" Residue "M PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "T GLU 7": "OE1" <-> "OE2" Residue "T TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 62": "OD1" <-> "OD2" Residue "U PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W ASP 40": "OD1" <-> "OD2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 99": "OE1" <-> "OE2" Residue "Y TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 94": "OD1" <-> "OD2" Residue "c GLU 75": "OE1" <-> "OE2" Residue "c PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 33": "OE1" <-> "OE2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "e TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 125": "OE1" <-> "OE2" Residue "h ASP 37": "OD1" <-> "OD2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 223": "OE1" <-> "OE2" Residue "h TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 269": "OE1" <-> "OE2" Residue "h ASP 304": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 78748 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': 142, 'rna2p_pyr': 111, 'rna3p_pur': 755, 'rna3p_pyr': 689} Link IDs: {'rna2p': 252, 'rna3p': 1444} 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: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 952 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1088 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "z" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3465 Classifications: {'RNA': 162} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 73, 'rna3p_pyr': 64} Link IDs: {'rna2p': 24, 'rna3p': 137} Chain breaks: 1 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69318 SG CYS b 23 93.931 129.505 136.507 1.00 38.78 S ATOM 69339 SG CYS b 26 97.538 130.902 138.596 1.00 40.02 S ATOM 69722 SG CYS b 74 94.988 127.560 137.621 1.00 39.58 S ATOM 69741 SG CYS b 77 95.256 128.735 139.767 1.00 34.58 S ATOM 72383 SG CYS g 121 150.488 98.244 242.455 1.00211.11 S ATOM 72419 SG CYS g 126 147.933 98.422 239.460 1.00225.10 S ATOM 72537 SG CYS g 141 150.017 99.740 239.460 1.00203.03 S ATOM 72556 SG CYS g 144 146.594 99.863 240.491 1.00203.40 S Time building chain proxies: 31.99, per 1000 atoms: 0.41 Number of scatterers: 78748 At special positions: 0 Unit cell: (234.65, 193.8, 260.3, 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 19827 8.00 N 14491 7.00 C 42390 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: 29.32 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " 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: 139 helices and 51 sheets defined 33.1% alpha, 14.1% beta 476 base pairs and 942 stacking pairs defined. Time for finding SS restraints: 22.66 Creating SS restraints... Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.738A pdb=" N ILE B 46 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 3.597A pdb=" N THR B 54 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.928A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 removed outlier: 4.206A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 removed outlier: 3.516A pdb=" N GLY B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.739A pdb=" N LEU B 201 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.770A pdb=" N GLY C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.983A pdb=" N GLU C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.567A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.811A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.756A pdb=" N ARG D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 85 Processing helix chain 'D' and resid 92 through 98 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 removed outlier: 3.679A pdb=" N PHE D 236 " --> pdb=" O THR D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.507A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 274 removed outlier: 3.554A pdb=" N GLU D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 162 through 168 removed outlier: 3.816A pdb=" N TYR E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL E 168 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 43 through 51 Processing helix chain 'F' and resid 59 through 67 Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 67 through 74 Processing helix chain 'G' and resid 86 through 104 Processing helix chain 'G' and resid 107 through 119 removed outlier: 3.563A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 removed outlier: 3.663A pdb=" N VAL G 147 " --> pdb=" O PRO G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.914A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 203 removed outlier: 4.122A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 237 removed outlier: 3.532A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 34 Processing helix chain 'I' and resid 71 through 75 removed outlier: 3.702A pdb=" N LYS I 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE I 75 " --> pdb=" O PHE I 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 71 through 75' 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: 4.255A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.790A pdb=" N GLU I 167 " --> pdb=" O ASN I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 182 Processing helix chain 'J' and resid 88 through 93 removed outlier: 3.728A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 115 Processing helix chain 'J' and resid 134 through 139 removed outlier: 3.521A pdb=" N LYS J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 155 removed outlier: 3.734A 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: 3.522A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY J 207 " --> pdb=" O LYS J 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 39 through 63 removed outlier: 4.258A 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 93 through 100 removed outlier: 3.532A pdb=" N ILE K 97 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU K 98 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU K 100 " --> pdb=" O ILE K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 108 removed outlier: 3.955A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 4.117A 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 171 through 184 Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.886A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 removed outlier: 3.512A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 84 Processing helix chain 'M' and resid 47 through 51 Processing helix chain 'N' and resid 15 through 29 Processing helix chain 'N' and resid 35 through 44 Processing helix chain 'N' and resid 61 through 70 Processing helix chain 'N' and resid 84 through 90 removed outlier: 4.393A pdb=" N TRP N 88 " --> pdb=" O LYS N 84 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL N 89 " --> pdb=" O LEU N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 130 Processing helix chain 'O' and resid 29 through 43 removed outlier: 3.850A pdb=" N VAL O 33 " --> pdb=" O THR O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 62 through 67 removed outlier: 3.547A pdb=" N VAL O 66 " --> pdb=" O GLN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 105 removed outlier: 4.518A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN O 105 " --> pdb=" O HIS O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 132 removed outlier: 3.956A pdb=" N ARG O 127 " --> pdb=" O HIS O 123 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.868A pdb=" N LYS P 61 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 57 through 62' Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 110 through 122 removed outlier: 4.062A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER P 122 " --> pdb=" O ALA P 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 5.186A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 46 removed outlier: 4.244A pdb=" N LEU Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'R' and resid 40 through 42 No H-bonds generated for 'chain 'R' and resid 40 through 42' 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: 3.967A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 114 removed outlier: 4.130A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 120 removed outlier: 3.768A pdb=" N LEU R 119 " --> pdb=" O ASP R 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 20 removed outlier: 3.684A pdb=" N LYS S 10 " --> pdb=" O THR S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 39 removed outlier: 3.784A pdb=" N ASN S 31 " --> pdb=" O ASP S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 64 Processing helix chain 'S' and resid 78 through 84 removed outlier: 3.560A pdb=" N TYR S 84 " --> pdb=" O ARG S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 110 removed outlier: 3.808A pdb=" N LEU S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP S 110 " --> pdb=" O LEU S 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 33 removed outlier: 3.879A pdb=" N THR T 31 " --> pdb=" O PHE T 28 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA T 32 " --> pdb=" O ALA T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 48 removed outlier: 4.227A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL T 44 " --> pdb=" O TYR T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.712A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 12 through 26 removed outlier: 4.049A 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 71 through 79 removed outlier: 4.001A pdb=" N ILE U 78 " --> pdb=" O SER U 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR U 79 " --> pdb=" O MET U 75 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 110 removed outlier: 3.903A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) 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 removed outlier: 3.620A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 4.011A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 77 removed outlier: 3.949A pdb=" N SER W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 44 removed outlier: 4.042A pdb=" N VAL X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 93 Processing helix chain 'X' and resid 113 through 120 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 24 through 31 Processing helix chain 'Y' and resid 33 through 39 Processing helix chain 'Y' and resid 130 through 136 Processing helix chain 'Z' and resid 36 through 48 removed outlier: 3.616A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 removed outlier: 3.777A pdb=" N ASN Z 85 " --> pdb=" O TYR Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 94 Processing helix chain 'Z' and resid 103 through 116 removed outlier: 3.654A pdb=" N ARG Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 126 Processing helix chain 'a' and resid 51 through 62 removed outlier: 3.915A pdb=" N TYR a 55 " --> pdb=" O ASP a 51 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 65 No H-bonds generated for 'chain 'a' and resid 63 through 65' Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 95 Processing helix chain 'b' and resid 49 through 56 Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.654A pdb=" N GLU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 8 removed outlier: 4.242A pdb=" N TRP e 8 " --> pdb=" O GLN e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.916A 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 'e' and resid 47 through 51 removed outlier: 3.773A pdb=" N ILE e 50 " --> pdb=" O ALA e 47 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY e 51 " --> pdb=" O LYS e 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 47 through 51' Processing helix chain 'f' and resid 105 through 115 Processing helix chain 'g' and resid 101 through 106 Processing helix chain 'n' and resid 2 through 24 removed outlier: 3.837A pdb=" N ARG n 6 " --> pdb=" O ARG n 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.670A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.821A pdb=" N THR C 98 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.821A pdb=" N THR C 98 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 13.359A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.151A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ARG C 213 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 209 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 138 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL C 215 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG C 136 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N MET C 217 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU C 134 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 137 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 102 through 112 removed outlier: 5.072A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY D 138 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.960A pdb=" N GLY D 119 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.726A pdb=" N VAL D 184 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 193 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N CYS D 188 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR D 224 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 34 through 42 removed outlier: 6.429A pdb=" N LEU E 51 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL E 37 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE E 49 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL E 39 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU E 47 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL E 41 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ARG E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 85 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 48 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR E 87 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU E 89 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 150 through 155 Processing sheet with id=AA9, first strand: chain 'E' and resid 223 through 226 removed outlier: 3.547A pdb=" N ILE E 223 " --> pdb=" O ILE h 189 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE h 189 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU E 225 " --> pdb=" O ASN h 187 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN h 187 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS h 175 " --> pdb=" O SER h 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 70 through 72 Processing sheet with id=AB2, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.808A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F 110 " --> pdb=" O ILE F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.661A pdb=" N VAL F 140 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR F 159 " --> pdb=" O ILE F 173 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP F 171 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 217 through 221 removed outlier: 6.676A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 229 through 230 removed outlier: 3.572A pdb=" N LYS F 233 " --> pdb=" O LYS F 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 140 through 141 removed outlier: 6.175A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.723A pdb=" N CYS H 12 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL H 108 " --> pdb=" O ASN H 56 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY H 54 " --> pdb=" O ASN H 110 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL H 112 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE H 52 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL H 114 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N VAL H 50 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.788A pdb=" N LYS H 93 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 47 through 51 removed outlier: 3.806A pdb=" N ALA I 47 " --> pdb=" O PHE I 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 93 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 185 through 188 removed outlier: 8.159A pdb=" N ASN I 186 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE I 154 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLU I 188 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL I 156 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE X 52 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL I 146 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE X 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE X 53 " --> pdb=" O LYS X 60 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS X 60 " --> pdb=" O ILE X 53 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 42 through 47 removed outlier: 6.853A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL J 46 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS J 54 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.653A pdb=" N CYS J 72 " --> pdb=" O TRP J 67 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU J 103 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL J 81 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE J 101 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLY J 187 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN J 64 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL J 189 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER J 66 " --> pdb=" O VAL J 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.729A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 61 through 63 Processing sheet with id=AC6, first strand: chain 'M' and resid 72 through 79 removed outlier: 6.123A pdb=" N VAL M 77 " --> pdb=" O ARG M 89 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG M 89 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS M 144 " --> pdb=" O THR M 127 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL M 128 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 91 through 93 Processing sheet with id=AC8, first strand: chain 'N' and resid 32 through 33 removed outlier: 3.664A pdb=" N VAL N 110 " --> pdb=" O ALA N 32 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 52 through 56 removed outlier: 7.187A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU P 93 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE P 129 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE P 95 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ASP P 131 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU P 97 " --> pdb=" O ASP P 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 75 through 77 removed outlier: 3.750A pdb=" N VAL Q 94 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR Q 101 " --> pdb=" O ASN Q 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 11 through 12 removed outlier: 3.965A pdb=" N VAL R 12 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS R 73 " --> pdb=" O THR R 20 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LYS R 33 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE R 68 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 96 through 98 removed outlier: 3.670A pdb=" N GLN S 118 " --> pdb=" O ILE S 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 12 through 15 Processing sheet with id=AD5, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.504A pdb=" N VAL V 54 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU V 88 " --> pdb=" O VAL V 54 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE V 84 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.504A pdb=" N VAL V 54 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU V 88 " --> pdb=" O VAL V 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR V 23 " --> pdb=" O GLU V 113 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 63 through 66 removed outlier: 3.573A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 35 through 36 removed outlier: 3.869A pdb=" N VAL W 36 " --> pdb=" O LYS W 51 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS W 51 " --> pdb=" O VAL W 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'X' and resid 71 through 72 removed outlier: 4.123A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE X 130 " --> pdb=" O LYS X 71 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE X 125 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR X 105 " --> pdb=" O ILE X 125 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY X 127 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 81 through 82 removed outlier: 6.701A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS Y 124 " --> pdb=" O LEU Y 101 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Y' and resid 57 through 58 removed outlier: 3.875A pdb=" N ARG Y 67 " --> pdb=" O VAL Y 57 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 6 through 15 removed outlier: 6.557A pdb=" N ILE Z 7 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU Z 28 " --> pdb=" O ILE Z 7 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR Z 9 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP Z 26 " --> pdb=" O THR Z 9 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LYS Z 11 " --> pdb=" O VAL Z 24 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL Z 24 " --> pdb=" O LYS Z 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET Z 13 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN Z 22 " --> pdb=" O MET Z 13 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY Z 71 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE Z 72 " --> pdb=" O PHE Z 58 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'b' and resid 20 through 21 Processing sheet with id=AE5, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.606A pdb=" N ILE b 36 " --> pdb=" O TYR b 73 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 43 through 47 removed outlier: 3.625A pdb=" N THR c 44 " --> pdb=" O VAL c 35 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP c 34 " --> pdb=" O ARG c 80 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER c 78 " --> pdb=" O LYS c 36 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 64 through 65 removed outlier: 3.697A pdb=" N GLN c 65 " --> pdb=" O ARG c 72 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG c 72 " --> pdb=" O GLN c 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'd' and resid 31 through 32 removed outlier: 3.720A pdb=" N LYS d 16 " --> pdb=" O ARG d 31 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'g' and resid 138 through 139 removed outlier: 3.562A pdb=" N HIS g 139 " --> pdb=" O TYR g 148 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR g 148 " --> pdb=" O HIS g 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'h' and resid 21 through 22 removed outlier: 3.534A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE h 40 " --> pdb=" O ALA h 58 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA h 58 " --> pdb=" O ILE h 40 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N MET h 42 " --> pdb=" O GLN h 56 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'h' and resid 66 through 71 removed outlier: 4.710A pdb=" N ALA h 78 " --> pdb=" O TRP h 90 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP h 90 " --> pdb=" O ALA h 78 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER h 80 " --> pdb=" O ARG h 88 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG h 88 " --> pdb=" O SER h 80 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER h 82 " --> pdb=" O THR h 86 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR h 86 " --> pdb=" O SER h 82 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG h 99 " --> pdb=" O LEU h 89 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'h' and resid 108 through 112 removed outlier: 3.906A pdb=" N SER h 110 " --> pdb=" O GLY h 123 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA h 112 " --> pdb=" O VAL h 121 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL h 121 " --> pdb=" O ALA h 112 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'h' and resid 195 through 200 removed outlier: 3.572A pdb=" N THR h 199 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS h 207 " --> pdb=" O TRP h 219 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.538A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 288 through 290 removed outlier: 3.840A pdb=" N SER h 288 " --> pdb=" O GLY h 301 " (cutoff:3.500A) 1305 hydrogen bonds defined for protein. 3735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1204 hydrogen bonds 2036 hydrogen bond angles 0 basepair planarities 476 basepair parallelities 942 stacking parallelities Total time for adding SS restraints: 62.42 Time building geometry restraints manager: 31.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10936 1.33 - 1.45: 32601 1.45 - 1.58: 36578 1.58 - 1.70: 3703 1.70 - 1.83: 274 Bond restraints: 84092 Sorted by residual: bond pdb=" C LEU O 45 " pdb=" N THR O 46 " ideal model delta sigma weight residual 1.329 1.412 -0.084 1.60e-02 3.91e+03 2.73e+01 bond pdb=" CA ALA D 118 " pdb=" CB ALA D 118 " ideal model delta sigma weight residual 1.526 1.478 0.048 1.76e-02 3.23e+03 7.36e+00 bond pdb=" C ILE C 189 " pdb=" N PRO C 190 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.53e+00 bond pdb=" CA ILE N 35 " pdb=" C ILE N 35 " ideal model delta sigma weight residual 1.523 1.544 -0.021 9.60e-03 1.09e+04 4.76e+00 bond pdb=" O5' G z 266 " pdb=" C5' G z 266 " ideal model delta sigma weight residual 1.420 1.451 -0.031 1.50e-02 4.44e+03 4.17e+00 ... (remaining 84087 not shown) Histogram of bond angle deviations from ideal: 97.04 - 104.90: 8767 104.90 - 112.75: 47540 112.75 - 120.61: 37516 120.61 - 128.46: 26095 128.46 - 136.31: 2516 Bond angle restraints: 122434 Sorted by residual: angle pdb=" C LEU O 45 " pdb=" N THR O 46 " pdb=" CA THR O 46 " ideal model delta sigma weight residual 120.49 132.08 -11.59 1.42e+00 4.96e-01 6.66e+01 angle pdb=" N ILE I 75 " pdb=" CA ILE I 75 " pdb=" C ILE I 75 " ideal model delta sigma weight residual 113.71 107.60 6.11 9.50e-01 1.11e+00 4.14e+01 angle pdb=" C ASP P 65 " pdb=" N ARG P 66 " pdb=" CA ARG P 66 " ideal model delta sigma weight residual 120.82 129.79 -8.97 1.50e+00 4.44e-01 3.58e+01 angle pdb=" N VAL B 7 " pdb=" CA VAL B 7 " pdb=" C VAL B 7 " ideal model delta sigma weight residual 112.83 107.40 5.43 9.90e-01 1.02e+00 3.01e+01 angle pdb=" C3' U 2 688 " pdb=" O3' U 2 688 " pdb=" P U 2 689 " ideal model delta sigma weight residual 120.20 128.19 -7.99 1.50e+00 4.44e-01 2.83e+01 ... (remaining 122429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 45068 35.91 - 71.81: 1654 71.81 - 107.72: 117 107.72 - 143.63: 13 143.63 - 179.54: 23 Dihedral angle restraints: 46875 sinusoidal: 32819 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 200.00 20.98 179.02 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 8.50 -168.50 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" O4' C 2 853 " pdb=" C1' C 2 853 " pdb=" N1 C 2 853 " pdb=" C2 C 2 853 " ideal model delta sinusoidal sigma weight residual 200.00 36.86 163.14 1 1.50e+01 4.44e-03 8.35e+01 ... (remaining 46872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 14071 0.081 - 0.162: 1017 0.162 - 0.243: 83 0.243 - 0.325: 18 0.325 - 0.406: 5 Chirality restraints: 15194 Sorted by residual: chirality pdb=" CB ILE F 45 " pdb=" CA ILE F 45 " pdb=" CG1 ILE F 45 " pdb=" CG2 ILE F 45 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA ASP E 162 " pdb=" N ASP E 162 " pdb=" C ASP E 162 " pdb=" CB ASP E 162 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB ILE H 121 " pdb=" CA ILE H 121 " pdb=" CG1 ILE H 121 " pdb=" CG2 ILE H 121 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 15191 not shown) Planarity restraints: 8632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 145 " 0.433 9.50e-02 1.11e+02 1.94e-01 2.40e+01 pdb=" NE ARG G 145 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG G 145 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG G 145 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 145 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 61 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO D 62 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO D 62 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 62 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 117 " 0.334 9.50e-02 1.11e+02 1.50e-01 1.50e+01 pdb=" NE ARG D 117 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 117 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG D 117 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 117 " 0.018 2.00e-02 2.50e+03 ... (remaining 8629 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 7604 2.73 - 3.27: 67243 3.27 - 3.82: 146743 3.82 - 4.36: 174885 4.36 - 4.90: 256669 Nonbonded interactions: 653144 Sorted by model distance: nonbonded pdb=" O2' G 21121 " pdb=" O ILE C 204 " model vdw 2.191 2.440 nonbonded pdb=" OP2 C 2 98 " pdb=" O2' A 2 426 " model vdw 2.251 2.440 nonbonded pdb=" O6 G z 307 " pdb=" O2 U z 329 " model vdw 2.252 3.040 nonbonded pdb=" O6 G z 307 " pdb=" C2 U z 329 " model vdw 2.258 3.260 nonbonded pdb=" OH TYR h 228 " pdb=" O LEU h 261 " model vdw 2.270 2.440 ... (remaining 653139 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 42390 2.51 5 N 14491 2.21 5 O 19827 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: 2.810 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: 17.870 Check model and map are aligned: 0.850 Convert atoms to be neutral: 0.510 Process input model: 215.420 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 242.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 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 : 0.004 0.084 84092 Z= 0.232 Angle : 0.865 14.625 122434 Z= 0.428 Chirality : 0.044 0.406 15194 Planarity : 0.007 0.194 8632 Dihedral : 15.838 179.535 37809 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.60 % Favored : 93.38 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.10), residues: 4821 helix: -1.73 (0.11), residues: 1462 sheet: -1.38 (0.20), residues: 660 loop : -2.39 (0.10), residues: 2699 *********************** 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 591 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 590 time to evaluate : 4.639 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: 591 average time/residue: 0.6985 time to fit residues: 710.3609 Evaluate side-chains 367 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 4.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4089 ------------------------------------------------------------------------------- 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: 10.0000 chunk 499 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 516 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 314 optimal weight: 20.0000 chunk 384 optimal weight: 10.0000 chunk 598 optimal weight: 9.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN D 136 HIS ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS H 110 ASN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 ASN ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN O 49 GLN ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 ASN T 73 ASN W 2 GLN W 47 ASN X 24 GLN Y 110 HIS Y 127 ASN e 3 HIS ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 84092 Z= 0.299 Angle : 0.736 10.888 122434 Z= 0.369 Chirality : 0.041 0.297 15194 Planarity : 0.006 0.099 8632 Dihedral : 16.233 179.467 27707 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.60 % Favored : 93.38 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.11), residues: 4821 helix: -0.73 (0.12), residues: 1497 sheet: -1.58 (0.18), residues: 744 loop : -2.30 (0.11), residues: 2580 *********************** 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 454 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 445 time to evaluate : 4.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 451 average time/residue: 0.7271 time to fit residues: 576.9681 Evaluate side-chains 339 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 4.467 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5783 time to fit residues: 6.5307 ------------------------------------------------------------------------------- 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: 7.9990 chunk 185 optimal weight: 3.9990 chunk 498 optimal weight: 5.9990 chunk 407 optimal weight: 4.9990 chunk 165 optimal weight: 30.0000 chunk 599 optimal weight: 30.0000 chunk 647 optimal weight: 30.0000 chunk 533 optimal weight: 3.9990 chunk 594 optimal weight: 30.0000 chunk 204 optimal weight: 2.9990 chunk 480 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN E 174 HIS F 142 HIS ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN U 83 GLN W 2 GLN X 24 GLN Y 127 ASN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 ASN ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 64 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 84092 Z= 0.182 Angle : 0.599 10.615 122434 Z= 0.305 Chirality : 0.037 0.256 15194 Planarity : 0.005 0.081 8632 Dihedral : 16.075 178.553 27707 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.72 % Favored : 94.25 % 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: -2.08 (0.11), residues: 4821 helix: -0.10 (0.13), residues: 1494 sheet: -1.47 (0.18), residues: 742 loop : -2.19 (0.11), residues: 2585 *********************** 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 498 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 494 time to evaluate : 4.441 Fit side-chains 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: 497 average time/residue: 0.6961 time to fit residues: 598.2586 Evaluate side-chains 361 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 4.449 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5354 time to fit residues: 6.3727 ------------------------------------------------------------------------------- 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: 8.9990 chunk 450 optimal weight: 10.0000 chunk 311 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 chunk 286 optimal weight: 9.9990 chunk 402 optimal weight: 3.9990 chunk 601 optimal weight: 5.9990 chunk 636 optimal weight: 9.9990 chunk 314 optimal weight: 0.9990 chunk 570 optimal weight: 0.8980 chunk 171 optimal weight: 30.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN D 120 GLN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN J 99 ASN ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Q 98 ASN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN b 72 HIS ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 187 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 84092 Z= 0.176 Angle : 0.586 10.694 122434 Z= 0.298 Chirality : 0.036 0.258 15194 Planarity : 0.005 0.069 8632 Dihedral : 16.055 178.688 27707 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.51 % Favored : 93.47 % Rotamer Outliers : 0.07 % 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: -1.87 (0.11), residues: 4821 helix: 0.19 (0.13), residues: 1489 sheet: -1.38 (0.18), residues: 739 loop : -2.13 (0.11), residues: 2593 *********************** 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 490 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 487 time to evaluate : 4.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 489 average time/residue: 0.7235 time to fit residues: 619.8265 Evaluate side-chains 369 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 368 time to evaluate : 4.591 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5821 time to fit residues: 6.8419 ------------------------------------------------------------------------------- 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: 0.0870 chunk 361 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 474 optimal weight: 20.0000 chunk 262 optimal weight: 9.9990 chunk 543 optimal weight: 7.9990 chunk 440 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 6.9990 chunk 571 optimal weight: 2.9990 chunk 160 optimal weight: 40.0000 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Q 24 GLN Q 98 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN X 44 HIS Y 23 HIS Y 127 ASN ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 84092 Z= 0.195 Angle : 0.606 10.798 122434 Z= 0.307 Chirality : 0.037 0.259 15194 Planarity : 0.005 0.089 8632 Dihedral : 16.136 179.387 27707 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.74 % Favored : 93.24 % 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: -1.87 (0.11), residues: 4821 helix: 0.24 (0.13), residues: 1492 sheet: -1.45 (0.18), residues: 765 loop : -2.14 (0.11), residues: 2564 *********************** 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 470 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 469 time to evaluate : 4.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 469 average time/residue: 0.7097 time to fit residues: 585.0752 Evaluate side-chains 344 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 4.531 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5078 ------------------------------------------------------------------------------- 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: 9.9990 chunk 573 optimal weight: 5.9990 chunk 125 optimal weight: 40.0000 chunk 373 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 637 optimal weight: 9.9990 chunk 529 optimal weight: 10.0000 chunk 295 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 3.9990 chunk 334 optimal weight: 40.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS D 120 GLN D 172 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN J 99 ASN K 111 GLN ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 ASN ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN b 72 HIS ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 84092 Z= 0.260 Angle : 0.695 11.099 122434 Z= 0.352 Chirality : 0.040 0.264 15194 Planarity : 0.006 0.074 8632 Dihedral : 16.518 178.468 27707 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.44 % Favored : 91.54 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.11), residues: 4821 helix: -0.02 (0.13), residues: 1481 sheet: -1.60 (0.18), residues: 763 loop : -2.25 (0.11), residues: 2577 *********************** 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 447 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 445 time to evaluate : 4.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 447 average time/residue: 0.7006 time to fit residues: 549.7829 Evaluate side-chains 335 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 4.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4325 ------------------------------------------------------------------------------- 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: 20.0000 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 8.9990 chunk 465 optimal weight: 20.0000 chunk 360 optimal weight: 7.9990 chunk 536 optimal weight: 6.9990 chunk 356 optimal weight: 8.9990 chunk 635 optimal weight: 0.8980 chunk 397 optimal weight: 5.9990 chunk 387 optimal weight: 10.0000 chunk 293 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN D 172 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN L 44 HIS ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN O 49 GLN ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN ** Z 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 84092 Z= 0.209 Angle : 0.636 10.912 122434 Z= 0.323 Chirality : 0.038 0.265 15194 Planarity : 0.005 0.074 8632 Dihedral : 16.429 179.930 27707 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.91 % Favored : 93.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.11), residues: 4821 helix: 0.05 (0.13), residues: 1486 sheet: -1.52 (0.18), residues: 751 loop : -2.19 (0.11), residues: 2584 *********************** 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 452 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 4.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.7219 time to fit residues: 566.8240 Evaluate side-chains 346 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 4.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4298 ------------------------------------------------------------------------------- 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: 8.9990 chunk 253 optimal weight: 0.7980 chunk 379 optimal weight: 0.7980 chunk 191 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 123 optimal weight: 20.0000 chunk 403 optimal weight: 8.9990 chunk 432 optimal weight: 8.9990 chunk 314 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 499 optimal weight: 20.0000 overall best weight: 5.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN D 172 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN I 91 HIS ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN V 85 HIS ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN ** Z 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 84092 Z= 0.217 Angle : 0.650 10.340 122434 Z= 0.329 Chirality : 0.039 0.270 15194 Planarity : 0.005 0.076 8632 Dihedral : 16.476 179.921 27707 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.11 % Favored : 91.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.11), residues: 4821 helix: 0.05 (0.13), residues: 1487 sheet: -1.50 (0.18), residues: 751 loop : -2.19 (0.11), residues: 2583 *********************** 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 431 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 4.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.7334 time to fit residues: 550.6867 Evaluate side-chains 338 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 4.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4023 ------------------------------------------------------------------------------- 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: 0.9990 chunk 608 optimal weight: 3.9990 chunk 555 optimal weight: 0.6980 chunk 591 optimal weight: 8.9990 chunk 356 optimal weight: 0.9980 chunk 257 optimal weight: 0.7980 chunk 464 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 534 optimal weight: 0.4980 chunk 559 optimal weight: 20.0000 chunk 589 optimal weight: 30.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 HIS D 136 HIS ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN O 49 GLN Q 114 HIS ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 GLN ** h 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 215 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.071 84092 Z= 0.129 Angle : 0.558 12.108 122434 Z= 0.282 Chirality : 0.035 0.268 15194 Planarity : 0.004 0.075 8632 Dihedral : 16.039 178.318 27707 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.96 % Favored : 95.02 % 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: -1.56 (0.12), residues: 4821 helix: 0.55 (0.13), residues: 1480 sheet: -1.26 (0.18), residues: 744 loop : -1.97 (0.12), residues: 2597 *********************** 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 486 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 4.583 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: 0 outliers final: 0 residues processed: 486 average time/residue: 0.7330 time to fit residues: 623.6207 Evaluate side-chains 361 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 4.554 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5665 ------------------------------------------------------------------------------- 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: 0.9990 chunk 625 optimal weight: 10.0000 chunk 382 optimal weight: 0.0010 chunk 296 optimal weight: 9.9990 chunk 435 optimal weight: 1.9990 chunk 656 optimal weight: 30.0000 chunk 604 optimal weight: 30.0000 chunk 522 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 403 optimal weight: 4.9990 chunk 320 optimal weight: 4.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 HIS D 120 GLN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN L 61 GLN ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN X 24 GLN Z 94 HIS b 72 HIS ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 215 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 84092 Z= 0.143 Angle : 0.552 9.910 122434 Z= 0.279 Chirality : 0.035 0.267 15194 Planarity : 0.004 0.071 8632 Dihedral : 15.983 178.681 27707 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.04 % Favored : 93.94 % Rotamer Outliers : 0.07 % 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: -1.50 (0.12), residues: 4821 helix: 0.62 (0.13), residues: 1478 sheet: -1.23 (0.18), residues: 752 loop : -1.96 (0.12), residues: 2591 ********************** 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 452 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 449 time to evaluate : 4.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 450 average time/residue: 0.7372 time to fit residues: 584.0468 Evaluate side-chains 355 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 4.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5196 ------------------------------------------------------------------------------- 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: 5.9990 chunk 556 optimal weight: 3.9990 chunk 160 optimal weight: 40.0000 chunk 482 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 30.0000 chunk 523 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 537 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 HIS D 172 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN G 118 ASN ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN O 49 GLN P 20 GLN X 24 GLN b 72 HIS ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.069491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.058392 restraints weight = 608606.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.058851 restraints weight = 375230.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.059394 restraints weight = 225289.483| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 84092 Z= 0.223 Angle : 0.650 9.717 122434 Z= 0.329 Chirality : 0.039 0.273 15194 Planarity : 0.005 0.078 8632 Dihedral : 16.338 179.883 27707 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.21 % Favored : 91.77 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.12), residues: 4821 helix: 0.25 (0.13), residues: 1482 sheet: -1.41 (0.18), residues: 764 loop : -2.07 (0.12), residues: 2575 =============================================================================== Job complete usr+sys time: 10622.44 seconds wall clock time: 192 minutes 53.63 seconds (11573.63 seconds total)