Starting phenix.real_space_refine (version: dev) on Thu Dec 15 12:21:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/12_2022/7syi_25529.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/12_2022/7syi_25529.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/7syi_25529/12_2022/7syi_25529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/12_2022/7syi_25529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/12_2022/7syi_25529.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syi_25529/12_2022/7syi_25529.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 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 40": "OE1" <-> "OE2" Residue "F ASP 73": "OD1" <-> "OD2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "L TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 116": "OD1" <-> "OD2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 87": "OE1" <-> "OE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "T PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 112": "OE1" <-> "OE2" Residue "V GLU 111": "OE1" <-> "OE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W ASP 76": "OD1" <-> "OD2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X ASP 54": "OD1" <-> "OD2" Residue "X ASP 85": "OD1" <-> "OD2" Residue "X GLU 114": "OE1" <-> "OE2" Residue "X PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 33": "OD1" <-> "OD2" Residue "b ASP 94": "OD1" <-> "OD2" Residue "h ASP 144": "OD1" <-> "OD2" Residue "h PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 78761 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 142, 'rna2p_pyr': 112, 'rna3p_pur': 755, 'rna3p_pyr': 688} Link IDs: {'rna2p': 253, 'rna3p': 1443} Chain breaks: 11 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 956 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "z" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3465 Classifications: {'RNA': 162} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 14, 'rna3p_pur': 74, 'rna3p_pyr': 64} Link IDs: {'rna2p': 23, 'rna3p': 138} Chain breaks: 1 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69331 SG CYS b 23 91.709 129.272 136.475 1.00 59.58 S ATOM 69352 SG CYS b 26 95.144 129.285 138.932 1.00 62.93 S ATOM 69735 SG CYS b 74 93.896 126.926 137.740 1.00 55.58 S ATOM 69754 SG CYS b 77 93.875 128.245 139.198 1.00 56.01 S ATOM 72396 SG CYS g 121 149.427 99.916 244.462 1.00304.65 S ATOM 72432 SG CYS g 126 147.259 97.880 243.091 1.00300.71 S ATOM 72550 SG CYS g 141 149.327 100.755 242.311 1.00295.58 S ATOM 72569 SG CYS g 144 145.544 100.279 242.161 1.00284.35 S Time building chain proxies: 33.49, per 1000 atoms: 0.43 Number of scatterers: 78761 At special positions: 0 Unit cell: (233.7, 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 19829 8.00 N 14495 7.00 C 42397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.40 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " 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 144 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " Number of angles added : 12 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9066 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 58 sheets defined 33.2% alpha, 15.2% beta 472 base pairs and 941 stacking pairs defined. Time for finding SS restraints: 21.94 Creating SS restraints... Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.441A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 removed outlier: 3.558A pdb=" N TYR B 37 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE B 38 " --> pdb=" O GLU B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 34 through 38' Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.502A pdb=" N GLY B 45 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 46 " --> pdb=" O SER B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 46' Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.783A pdb=" N VAL B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.570A pdb=" N LEU B 201 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 23 through 28 removed outlier: 3.724A pdb=" N LYS C 27 " --> pdb=" O PRO C 24 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 28 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.819A pdb=" N MET C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.832A pdb=" N GLU C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.941A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 77 through 84 removed outlier: 4.158A pdb=" N ILE D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.588A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.611A pdb=" N ALA D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 218 removed outlier: 3.651A pdb=" N GLY D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 264 through 277 removed outlier: 5.524A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 97 through 109 removed outlier: 3.635A pdb=" N GLN E 101 " --> pdb=" O CYS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.924A pdb=" N VAL E 164 " --> pdb=" O GLY E 161 " (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 66 Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 32 through 36 Processing helix chain 'G' and resid 67 through 76 removed outlier: 4.554A pdb=" N THR G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 105 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.740A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN G 118 " --> pdb=" O ASN G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 179 removed outlier: 3.541A pdb=" N CYS G 172 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN G 179 " --> pdb=" O ASP G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 203 removed outlier: 4.255A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 25 removed outlier: 3.859A pdb=" N ARG H 25 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 153 through 157 removed outlier: 3.812A pdb=" N VAL H 157 " --> pdb=" O ARG H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 236 removed outlier: 3.503A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 34 removed outlier: 3.686A pdb=" N SER I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER I 34 " --> pdb=" O LEU I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 87 removed outlier: 3.597A pdb=" N LEU I 79 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.910A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.854A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 117 Processing helix chain 'J' and resid 132 through 139 removed outlier: 4.015A pdb=" N ILE J 136 " --> pdb=" O GLU J 132 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.500A pdb=" N GLN J 146 " --> pdb=" O SER J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 192 through 207 removed outlier: 4.193A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 36 Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.406A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 85 Processing helix chain 'K' and resid 96 through 100 Processing helix chain 'K' and resid 101 through 107 removed outlier: 4.052A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 Processing helix chain 'K' and resid 122 through 131 Processing helix chain 'K' and resid 150 through 154 removed outlier: 4.131A pdb=" N GLN K 154 " --> pdb=" O LEU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 167 removed outlier: 3.788A pdb=" N GLY K 167 " --> pdb=" O PRO K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 185 Processing helix chain 'L' and resid 4 through 18 Processing helix chain 'L' and resid 41 through 56 removed outlier: 4.183A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'M' and resid 47 through 51 Processing helix chain 'N' and resid 15 through 29 Processing helix chain 'N' and resid 34 through 44 Processing helix chain 'N' and resid 60 through 70 removed outlier: 3.829A pdb=" N LEU N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 88 removed outlier: 3.711A pdb=" N GLU N 87 " --> pdb=" O LYS N 84 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP N 88 " --> pdb=" O LEU N 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 88' Processing helix chain 'N' and resid 120 through 130 Processing helix chain 'O' and resid 29 through 44 removed outlier: 4.067A pdb=" N VAL O 33 " --> pdb=" O THR O 29 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY O 44 " --> pdb=" O LEU O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 59 Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 104 removed outlier: 4.245A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 132 removed outlier: 3.729A pdb=" N ARG O 127 " --> pdb=" O HIS O 123 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 62 removed outlier: 4.400A pdb=" N VAL P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 62' Processing helix chain 'P' and resid 70 through 89 removed outlier: 3.714A pdb=" N ALA P 74 " --> pdb=" O SER P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 122 removed outlier: 3.533A pdb=" N SER P 122 " --> pdb=" O ALA P 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 20 removed outlier: 4.075A pdb=" N GLY Q 19 " --> pdb=" O THR Q 16 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL Q 20 " --> pdb=" O TYR Q 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 16 through 20' Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.918A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 47 removed outlier: 3.566A pdb=" N LEU Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG Q 47 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'R' and resid 47 through 59 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 76 through 99 removed outlier: 4.006A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.788A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 20 removed outlier: 3.739A pdb=" N LYS S 10 " --> pdb=" O THR S 6 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 39 removed outlier: 3.711A 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 99 through 108 Processing helix chain 'T' and resid 25 through 30 removed outlier: 4.239A pdb=" N ILE T 30 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.536A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS T 47 " --> pdb=" O VAL T 43 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 removed outlier: 3.753A pdb=" N VAL T 64 " --> pdb=" O THR T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 78 Processing helix chain 'T' and resid 99 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 10 through 26 removed outlier: 4.390A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 4.332A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 78 removed outlier: 3.739A pdb=" N LYS U 77 " --> pdb=" O GLY U 73 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE U 78 " --> pdb=" O SER U 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 73 through 78' Processing helix chain 'U' and resid 96 through 110 removed outlier: 3.991A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 143 removed outlier: 3.620A pdb=" N GLN U 128 " --> pdb=" O THR U 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 46 Processing helix chain 'V' and resid 94 through 103 Processing helix chain 'W' and resid 56 through 63 Processing helix chain 'W' and resid 65 through 77 Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 44 Processing helix chain 'X' and resid 85 through 93 removed outlier: 3.544A pdb=" N TRP X 89 " --> pdb=" O ASP X 85 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN X 92 " --> pdb=" O LYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 120 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 25 through 30 Processing helix chain 'Y' and resid 32 through 39 removed outlier: 4.100A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 48 removed outlier: 4.437A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 removed outlier: 3.922A pdb=" N ASN Z 85 " --> pdb=" O TYR Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 94 removed outlier: 3.595A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 117 removed outlier: 3.583A pdb=" N ARG Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL Z 117 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 126 removed outlier: 3.626A pdb=" N GLY Z 126 " --> pdb=" O LYS Z 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 62 Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 95 removed outlier: 3.585A pdb=" N ALA a 84 " --> pdb=" O ARG a 80 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG a 85 " --> pdb=" O GLY a 81 " (cutoff:3.500A) 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: 3.888A pdb=" N GLU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS c 18 " --> pdb=" O GLU c 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 14 through 19 removed outlier: 3.980A pdb=" N SER e 18 " --> pdb=" O PHE e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 46 Processing helix chain 'e' and resid 47 through 51 removed outlier: 3.564A pdb=" N GLY e 51 " --> pdb=" O LYS e 48 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 105 through 115 Processing helix chain 'g' and resid 100 through 105 removed outlier: 3.723A pdb=" N LEU g 103 " --> pdb=" O LEU g 100 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 24 Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.097A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 31 through 32 Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 69 removed outlier: 3.557A pdb=" N GLY C 102 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 121 through 128 removed outlier: 3.717A pdb=" N ALA C 123 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL C 140 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL C 212 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N PHE C 142 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL C 210 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 104 through 112 removed outlier: 5.793A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 128 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 137 through 138 Processing sheet with id=AA7, first strand: chain 'D' and resid 185 through 188 Processing sheet with id=AA8, first strand: chain 'D' and resid 196 through 197 Processing sheet with id=AA9, first strand: chain 'E' and resid 34 through 40 removed outlier: 3.529A pdb=" N GLU E 47 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR E 46 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N TYR E 87 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE E 48 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLU E 89 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE E 50 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 150 through 152 removed outlier: 3.568A pdb=" N MET E 150 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE E 188 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 150 through 152 removed outlier: 3.568A pdb=" N MET E 150 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 224 through 226 removed outlier: 5.553A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR h 186 " --> pdb=" O VAL h 176 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE h 165 " --> pdb=" O TRP h 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 71 through 72 removed outlier: 4.551A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 102 through 103 removed outlier: 3.927A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 136 through 141 removed outlier: 3.599A pdb=" N ILE F 136 " --> pdb=" O GLY F 132 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP F 171 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 217 through 221 removed outlier: 3.884A pdb=" N GLY F 193 " --> pdb=" O CYS F 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AB9, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AC1, first strand: chain 'G' and resid 123 through 124 removed outlier: 7.521A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG d 44 " --> pdb=" O VAL d 30 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL d 30 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY d 19 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG d 31 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL d 17 " --> pdb=" O ARG d 31 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N GLU d 33 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR d 15 " --> pdb=" O GLU d 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.811A pdb=" N CYS H 12 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY H 54 " --> pdb=" O ASN H 110 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL H 112 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE H 52 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL H 114 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL H 50 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.600A pdb=" N VAL H 73 " --> pdb=" O VAL H 97 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 48 through 53 removed outlier: 3.514A pdb=" N ILE I 51 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA I 59 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG I 57 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 48 through 53 removed outlier: 3.514A pdb=" N ILE I 51 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA I 59 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG I 57 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE I 95 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE I 62 " --> pdb=" O ILE I 95 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 184 through 188 removed outlier: 6.726A pdb=" N ARG I 152 " --> pdb=" O ASP I 184 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASN I 186 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE I 154 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLU I 188 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL I 156 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE I 144 " --> pdb=" O ILE X 52 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE X 52 " --> pdb=" O ILE I 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.859A pdb=" N ILE J 3 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 42 through 47 removed outlier: 6.691A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.760A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG J 74 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG J 77 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU J 103 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL J 81 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE J 101 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL J 62 " --> pdb=" O ALA J 185 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLY J 187 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN J 64 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL J 189 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER J 66 " --> pdb=" O VAL J 189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.848A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 20 through 23 removed outlier: 4.051A pdb=" N MET L 21 " --> pdb=" O TRP L 69 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TRP L 69 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA L 23 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE L 67 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 72 through 73 removed outlier: 3.648A pdb=" N LYS M 144 " --> pdb=" O THR M 127 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 10.983A pdb=" N PHE M 140 " --> pdb=" O ASN M 108 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N SER M 110 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL M 142 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N HIS M 112 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LYS M 144 " --> pdb=" O HIS M 112 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG M 105 " --> pdb=" O TYR M 92 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG M 90 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 49 through 52 removed outlier: 4.376A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL N 111 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL N 109 " --> pdb=" O VAL N 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 52 through 57 removed outlier: 3.866A pdb=" N CYS P 54 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS P 43 " --> pdb=" O HIS P 32 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY P 29 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS P 96 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS P 31 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG P 98 " --> pdb=" O CYS P 31 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE P 33 " --> pdb=" O ARG P 98 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU P 93 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE P 129 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE P 95 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASP P 131 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU P 97 " --> pdb=" O ASP P 131 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 77 through 78 removed outlier: 3.545A pdb=" N TYR Q 97 " --> pdb=" O THR Q 78 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.582A pdb=" N GLY R 14 " --> pdb=" O ALA R 21 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA R 21 " --> pdb=" O GLY R 14 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.582A pdb=" N GLY R 14 " --> pdb=" O ALA R 21 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA R 21 " --> pdb=" O GLY R 14 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR R 20 " --> pdb=" O LYS R 73 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS R 73 " --> pdb=" O THR R 20 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 33 through 34 Processing sheet with id=AE1, first strand: chain 'S' and resid 97 through 98 removed outlier: 6.185A pdb=" N GLN S 118 " --> pdb=" O VAL S 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'U' and resid 81 through 83 removed outlier: 4.424A pdb=" N GLY U 81 " --> pdb=" O SER U 93 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER U 93 " --> pdb=" O GLY U 81 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS U 91 " --> pdb=" O GLN U 83 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 51 through 55 removed outlier: 5.365A pdb=" N GLY V 52 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP V 90 " --> pdb=" O GLY V 52 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 61 through 66 removed outlier: 3.910A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP V 78 " --> pdb=" O THR V 65 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 32 through 36 Processing sheet with id=AE6, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.787A pdb=" N LEU X 126 " --> pdb=" O VAL X 103 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET X 111 " --> pdb=" O LEU X 104 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 80 through 82 removed outlier: 6.297A pdb=" N ARG Y 67 " --> pdb=" O GLY Y 56 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLY Y 56 " --> pdb=" O ARG Y 67 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS Y 69 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LYS Y 54 " --> pdb=" O CYS Y 69 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU Y 52 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY Y 49 " --> pdb=" O VAL Y 100 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 6 through 15 removed outlier: 4.805A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE Z 72 " --> pdb=" O PHE Z 58 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE Z 58 " --> pdb=" O PHE Z 72 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 6 through 15 removed outlier: 4.805A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'a' and resid 67 through 68 removed outlier: 3.765A pdb=" N ILE a 68 " --> pdb=" O TYR a 109 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AF3, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.670A pdb=" N ILE b 36 " --> pdb=" O TYR b 73 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'c' and resid 43 through 47 removed outlier: 3.547A pdb=" N MET c 33 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP c 34 " --> pdb=" O ARG c 80 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 54 through 55 removed outlier: 3.768A pdb=" N VAL c 54 " --> pdb=" O CYS c 64 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 138 through 140 Processing sheet with id=AF7, first strand: chain 'h' and resid 5 through 11 removed outlier: 5.414A pdb=" N LEU h 7 " --> pdb=" O GLN h 311 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLN h 311 " --> pdb=" O LEU h 7 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 21 through 22 removed outlier: 3.524A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE h 41 " --> pdb=" O SER h 33 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET h 42 " --> pdb=" O ARG h 57 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG h 57 " --> pdb=" O MET h 42 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 66 through 71 Processing sheet with id=AG1, first strand: chain 'h' and resid 86 through 89 removed outlier: 3.900A pdb=" N ARG h 99 " --> pdb=" O LEU h 89 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 108 through 112 removed outlier: 3.606A pdb=" N SER h 122 " --> pdb=" O LYS h 130 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE h 129 " --> pdb=" O VAL h 142 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 197 through 200 removed outlier: 3.622A pdb=" N THR h 199 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS h 207 " --> pdb=" O TRP h 219 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET h 217 " --> pdb=" O SER h 209 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 239 through 241 removed outlier: 3.678A pdb=" N CYS h 240 " --> pdb=" O CYS h 249 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE h 256 " --> pdb=" O GLU h 269 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU h 269 " --> pdb=" O ILE h 256 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE h 258 " --> pdb=" O VAL h 267 " (cutoff:3.500A) 1318 hydrogen bonds defined for protein. 3732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1197 hydrogen bonds 2002 hydrogen bond angles 0 basepair planarities 472 basepair parallelities 941 stacking parallelities Total time for adding SS restraints: 60.01 Time building geometry restraints manager: 34.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 7023 1.24 - 1.39: 23628 1.39 - 1.53: 47771 1.53 - 1.68: 5409 1.68 - 1.83: 274 Bond restraints: 84105 Sorted by residual: bond pdb=" CG PRO S 122 " pdb=" CD PRO S 122 " ideal model delta sigma weight residual 1.503 1.096 0.407 3.40e-02 8.65e+02 1.43e+02 bond pdb=" CB PRO S 122 " pdb=" CG PRO S 122 " ideal model delta sigma weight residual 1.492 1.186 0.306 5.00e-02 4.00e+02 3.74e+01 bond pdb=" C ILE C 189 " pdb=" N PRO C 190 " ideal model delta sigma weight residual 1.326 1.374 -0.048 1.44e-02 4.82e+03 1.10e+01 bond pdb=" N PRO S 122 " pdb=" CD PRO S 122 " ideal model delta sigma weight residual 1.473 1.514 -0.041 1.40e-02 5.10e+03 8.45e+00 bond pdb=" CA GLU C 68 " pdb=" CB GLU C 68 " ideal model delta sigma weight residual 1.525 1.566 -0.042 1.47e-02 4.63e+03 8.07e+00 ... (remaining 84100 not shown) Histogram of bond angle deviations from ideal: 76.03 - 90.66: 2 90.66 - 105.29: 9177 105.29 - 119.92: 78370 119.92 - 134.54: 34891 134.54 - 149.17: 9 Bond angle restraints: 122449 Sorted by residual: angle pdb=" N PRO S 122 " pdb=" CD PRO S 122 " pdb=" CG PRO S 122 " ideal model delta sigma weight residual 103.20 76.03 27.17 1.50e+00 4.44e-01 3.28e+02 angle pdb=" CB PRO S 122 " pdb=" CG PRO S 122 " pdb=" CD PRO S 122 " ideal model delta sigma weight residual 106.10 149.17 -43.07 3.20e+00 9.77e-02 1.81e+02 angle pdb=" CA PRO S 122 " pdb=" CB PRO S 122 " pdb=" CG PRO S 122 " ideal model delta sigma weight residual 104.50 80.30 24.20 1.90e+00 2.77e-01 1.62e+02 angle pdb=" CA PRO S 122 " pdb=" N PRO S 122 " pdb=" CD PRO S 122 " ideal model delta sigma weight residual 112.00 102.71 9.29 1.40e+00 5.10e-01 4.40e+01 angle pdb=" C GLU I 31 " pdb=" N MET I 32 " pdb=" CA MET I 32 " ideal model delta sigma weight residual 121.92 111.90 10.02 1.73e+00 3.34e-01 3.36e+01 ... (remaining 122444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 45225 35.95 - 71.90: 1499 71.90 - 107.85: 128 107.85 - 143.80: 9 143.80 - 179.75: 25 Dihedral angle restraints: 46886 sinusoidal: 32830 harmonic: 14056 Sorted by residual: dihedral pdb=" O4' U 21624 " pdb=" C1' U 21624 " pdb=" N1 U 21624 " pdb=" C2 U 21624 " ideal model delta sinusoidal sigma weight residual 200.00 23.51 176.49 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual 200.00 37.96 162.04 1 1.50e+01 4.44e-03 8.33e+01 dihedral pdb=" O4' C 21518 " pdb=" C1' C 21518 " pdb=" N1 C 21518 " pdb=" C2 C 21518 " ideal model delta sinusoidal sigma weight residual 200.00 43.28 156.72 1 1.50e+01 4.44e-03 8.19e+01 ... (remaining 46883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 14673 0.106 - 0.212: 483 0.212 - 0.319: 30 0.319 - 0.425: 7 0.425 - 0.531: 1 Chirality restraints: 15194 Sorted by residual: chirality pdb=" CB ILE R 32 " pdb=" CA ILE R 32 " pdb=" CG1 ILE R 32 " pdb=" CG2 ILE R 32 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" CB VAL B 66 " pdb=" CA VAL B 66 " pdb=" CG1 VAL B 66 " pdb=" CG2 VAL B 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.01e+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 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 15191 not shown) Planarity restraints: 8634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 64 " 0.031 2.00e-02 2.50e+03 3.26e-02 2.66e+01 pdb=" CG TRP L 64 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP L 64 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP L 64 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP L 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 64 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 64 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 64 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP L 64 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21753 " -0.035 2.00e-02 2.50e+03 2.75e-02 1.70e+01 pdb=" N1 C 21753 " 0.043 2.00e-02 2.50e+03 pdb=" C2 C 21753 " -0.046 2.00e-02 2.50e+03 pdb=" O2 C 21753 " 0.035 2.00e-02 2.50e+03 pdb=" N3 C 21753 " -0.000 2.00e-02 2.50e+03 pdb=" C4 C 21753 " -0.015 2.00e-02 2.50e+03 pdb=" N4 C 21753 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C 21753 " 0.007 2.00e-02 2.50e+03 pdb=" C6 C 21753 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN S 121 " -0.061 5.00e-02 4.00e+02 8.68e-02 1.20e+01 pdb=" N PRO S 122 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO S 122 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO S 122 " -0.046 5.00e-02 4.00e+02 ... (remaining 8631 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 9672 2.75 - 3.29: 67315 3.29 - 3.83: 149291 3.83 - 4.36: 173426 4.36 - 4.90: 255070 Nonbonded interactions: 654774 Sorted by model distance: nonbonded pdb=" O2' G 21121 " pdb=" O ILE C 204 " model vdw 2.213 2.440 nonbonded pdb=" OE1 GLU F 40 " pdb=" OH TYR F 103 " model vdw 2.240 2.440 nonbonded pdb=" O2 U z 262 " pdb=" O6 G z 271 " model vdw 2.255 2.432 nonbonded pdb=" OP1 U 21549 " pdb=" OH TYR e 34 " model vdw 2.258 2.440 nonbonded pdb=" O2' A 21276 " pdb=" OG SER L 54 " model vdw 2.264 2.440 ... (remaining 654769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1858 5.49 5 S 180 5.16 5 C 42397 2.51 5 N 14495 2.21 5 O 19829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 0.140 Extract box with map and model: 18.570 Check model and map are aligned: 0.900 Convert atoms to be neutral: 0.530 Process input model: 218.590 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 246.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 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 0.407 84105 Z= 0.254 Angle : 0.868 43.073 122449 Z= 0.423 Chirality : 0.043 0.531 15194 Planarity : 0.006 0.108 8634 Dihedral : 15.560 179.753 37820 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.32 % 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: -2.89 (0.11), residues: 4821 helix: -1.82 (0.11), residues: 1447 sheet: -1.30 (0.19), residues: 726 loop : -2.18 (0.11), residues: 2648 *********************** 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 628 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 628 time to evaluate : 4.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 628 average time/residue: 0.7252 time to fit residues: 778.2766 Evaluate side-chains 431 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 4.712 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 556 optimal weight: 20.0000 chunk 499 optimal weight: 30.0000 chunk 277 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 chunk 266 optimal weight: 0.0670 chunk 516 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 314 optimal weight: 1.9990 chunk 384 optimal weight: 0.9980 chunk 598 optimal weight: 5.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS D 172 ASN E 74 GLN E 101 GLN F 201 HIS G 79 HIS ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN Q 104 GLN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 137 GLN ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.080 84105 Z= 0.125 Angle : 0.537 10.246 122449 Z= 0.270 Chirality : 0.033 0.214 15194 Planarity : 0.004 0.057 8634 Dihedral : 15.486 179.564 27708 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.33 % Favored : 94.65 % 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: -2.03 (0.11), residues: 4821 helix: -0.50 (0.13), residues: 1472 sheet: -1.21 (0.18), residues: 784 loop : -1.93 (0.12), residues: 2565 *********************** 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 564 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 560 time to evaluate : 4.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 563 average time/residue: 0.7530 time to fit residues: 742.3941 Evaluate side-chains 414 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 4.690 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5881 ------------------------------------------------------------------------------- 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: 8.9990 chunk 185 optimal weight: 20.0000 chunk 498 optimal weight: 10.0000 chunk 407 optimal weight: 8.9990 chunk 165 optimal weight: 30.0000 chunk 599 optimal weight: 4.9990 chunk 647 optimal weight: 30.0000 chunk 533 optimal weight: 5.9990 chunk 594 optimal weight: 40.0000 chunk 204 optimal weight: 9.9990 chunk 480 optimal weight: 4.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS D 172 ASN G 79 HIS G 82 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 84105 Z= 0.263 Angle : 0.668 10.542 122449 Z= 0.335 Chirality : 0.038 0.250 15194 Planarity : 0.006 0.073 8634 Dihedral : 15.927 179.729 27708 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.76 % Favored : 92.22 % Rotamer Outliers : 0.12 % 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: -1.96 (0.11), residues: 4821 helix: -0.22 (0.13), residues: 1473 sheet: -1.52 (0.18), residues: 751 loop : -1.90 (0.12), residues: 2597 *********************** 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 523 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 518 time to evaluate : 4.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 523 average time/residue: 0.7078 time to fit residues: 640.4275 Evaluate side-chains 385 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 383 time to evaluate : 4.707 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5310 time to fit residues: 7.6704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 592 optimal weight: 4.9990 chunk 450 optimal weight: 9.9990 chunk 311 optimal weight: 0.0980 chunk 66 optimal weight: 20.0000 chunk 286 optimal weight: 7.9990 chunk 402 optimal weight: 20.0000 chunk 601 optimal weight: 0.9990 chunk 636 optimal weight: 0.6980 chunk 314 optimal weight: 4.9990 chunk 570 optimal weight: 0.7980 chunk 171 optimal weight: 30.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN D 136 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** F 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 HIS G 36 GLN G 79 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 HIS ** I 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 76 HIS ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 188 HIS h 285 GLN ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.074 84105 Z= 0.130 Angle : 0.532 10.108 122449 Z= 0.268 Chirality : 0.033 0.212 15194 Planarity : 0.004 0.071 8634 Dihedral : 15.677 178.975 27708 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.14 % Favored : 94.84 % 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: -1.57 (0.12), residues: 4821 helix: 0.22 (0.14), residues: 1475 sheet: -1.32 (0.18), residues: 753 loop : -1.73 (0.12), 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 565 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 564 time to evaluate : 4.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 565 average time/residue: 0.7299 time to fit residues: 714.4409 Evaluate side-chains 406 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 4.767 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.7985 ------------------------------------------------------------------------------- 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: 0.6980 chunk 361 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 474 optimal weight: 9.9990 chunk 262 optimal weight: 0.2980 chunk 543 optimal weight: 20.0000 chunk 440 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 571 optimal weight: 6.9990 chunk 160 optimal weight: 30.0000 overall best weight: 5.1986 ------------------------------------------------------------------------------- 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 D 172 ASN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS G 82 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 28 HIS f 117 ASN ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 84105 Z= 0.212 Angle : 0.600 10.396 122449 Z= 0.301 Chirality : 0.036 0.215 15194 Planarity : 0.005 0.068 8634 Dihedral : 15.880 179.903 27708 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.82 % Favored : 92.16 % 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: -1.69 (0.12), residues: 4821 helix: 0.13 (0.13), residues: 1484 sheet: -1.45 (0.18), residues: 774 loop : -1.79 (0.12), residues: 2563 *********************** 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 514 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 513 time to evaluate : 4.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 514 average time/residue: 0.7159 time to fit residues: 637.0443 Evaluate side-chains 388 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 387 time to evaluate : 4.668 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6206 time to fit residues: 6.6657 ------------------------------------------------------------------------------- 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: 0.9990 chunk 573 optimal weight: 8.9990 chunk 125 optimal weight: 40.0000 chunk 373 optimal weight: 0.5980 chunk 157 optimal weight: 30.0000 chunk 637 optimal weight: 10.0000 chunk 529 optimal weight: 2.9990 chunk 295 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 7.9990 chunk 334 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN G 79 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 ASN ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS I 186 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 28 HIS e 45 GLN ** f 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 187 ASN ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 84105 Z= 0.151 Angle : 0.551 10.269 122449 Z= 0.277 Chirality : 0.034 0.214 15194 Planarity : 0.004 0.071 8634 Dihedral : 15.815 179.124 27708 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.08 % Favored : 93.90 % 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: -1.52 (0.12), residues: 4821 helix: 0.30 (0.14), residues: 1481 sheet: -1.40 (0.18), residues: 760 loop : -1.69 (0.12), residues: 2580 *********************** 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 528 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 6.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.7127 time to fit residues: 650.0972 Evaluate side-chains 397 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 4.682 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5791 ------------------------------------------------------------------------------- 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: 4.9990 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 10.0000 chunk 465 optimal weight: 5.9990 chunk 360 optimal weight: 8.9990 chunk 536 optimal weight: 7.9990 chunk 356 optimal weight: 3.9990 chunk 635 optimal weight: 40.0000 chunk 397 optimal weight: 9.9990 chunk 387 optimal weight: 9.9990 chunk 293 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS G 82 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN X 16 ASN e 45 GLN f 117 ASN ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 187 ASN ** h 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 84105 Z= 0.247 Angle : 0.653 10.665 122449 Z= 0.328 Chirality : 0.038 0.221 15194 Planarity : 0.005 0.066 8634 Dihedral : 16.189 179.492 27708 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.59 % Favored : 91.39 % 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: -1.80 (0.12), residues: 4821 helix: 0.02 (0.13), residues: 1474 sheet: -1.55 (0.18), residues: 765 loop : -1.83 (0.12), residues: 2582 *********************** 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 510 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 5.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.7356 time to fit residues: 649.3900 Evaluate side-chains 396 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 4.703 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6130 ------------------------------------------------------------------------------- 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: 10.0000 chunk 253 optimal weight: 0.9980 chunk 379 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 124 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 403 optimal weight: 30.0000 chunk 432 optimal weight: 1.9990 chunk 314 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 499 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS J 138 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 45 GLN ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 84105 Z= 0.174 Angle : 0.586 10.369 122449 Z= 0.295 Chirality : 0.036 0.235 15194 Planarity : 0.004 0.065 8634 Dihedral : 16.068 179.601 27708 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.55 % Favored : 93.42 % 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: -1.71 (0.12), residues: 4821 helix: 0.09 (0.13), residues: 1489 sheet: -1.57 (0.18), residues: 779 loop : -1.76 (0.12), residues: 2553 *********************** 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 519 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 4.905 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: 519 average time/residue: 0.7519 time to fit residues: 673.3206 Evaluate side-chains 404 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 4.687 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6018 ------------------------------------------------------------------------------- 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: 5.9990 chunk 555 optimal weight: 0.0000 chunk 591 optimal weight: 0.0870 chunk 356 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 464 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 534 optimal weight: 2.9990 chunk 559 optimal weight: 4.9990 chunk 589 optimal weight: 20.0000 overall best weight: 1.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN D 120 GLN D 136 HIS ** F 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS G 82 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 35 ASN R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN Y 20 GLN Y 23 HIS ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 117 ASN ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.065 84105 Z= 0.131 Angle : 0.541 11.388 122449 Z= 0.272 Chirality : 0.034 0.240 15194 Planarity : 0.004 0.059 8634 Dihedral : 15.851 179.815 27708 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.35 % Favored : 93.63 % 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: -1.46 (0.12), residues: 4821 helix: 0.35 (0.14), residues: 1486 sheet: -1.38 (0.18), residues: 782 loop : -1.65 (0.12), residues: 2553 *********************** 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 536 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 535 time to evaluate : 4.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 536 average time/residue: 0.7371 time to fit residues: 678.3375 Evaluate side-chains 415 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 5.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5753 ------------------------------------------------------------------------------- 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: 2.9990 chunk 625 optimal weight: 9.9990 chunk 382 optimal weight: 0.9990 chunk 296 optimal weight: 7.9990 chunk 435 optimal weight: 20.0000 chunk 656 optimal weight: 30.0000 chunk 604 optimal weight: 0.9990 chunk 522 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 403 optimal weight: 30.0000 chunk 320 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS ** I 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN e 28 HIS ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 84105 Z= 0.162 Angle : 0.561 11.241 122449 Z= 0.280 Chirality : 0.034 0.248 15194 Planarity : 0.004 0.056 8634 Dihedral : 15.897 179.868 27708 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.89 % Favored : 93.09 % 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: -1.44 (0.12), residues: 4821 helix: 0.39 (0.14), residues: 1482 sheet: -1.38 (0.18), residues: 775 loop : -1.65 (0.12), residues: 2564 ********************** 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 502 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 4.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.7308 time to fit residues: 635.1717 Evaluate side-chains 405 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 4.726 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6442 ------------------------------------------------------------------------------- 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: 9.9990 chunk 556 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 chunk 482 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 30.0000 chunk 523 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 537 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN D 136 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 HIS G 82 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS I 157 HIS ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 28 HIS e 45 GLN f 117 ASN ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.067999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.056058 restraints weight = 595653.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.056950 restraints weight = 341100.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.057372 restraints weight = 205365.376| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 84105 Z= 0.255 Angle : 0.668 12.009 122449 Z= 0.334 Chirality : 0.039 0.259 15194 Planarity : 0.005 0.065 8634 Dihedral : 16.278 179.766 27708 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.36 % Favored : 91.62 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.12), residues: 4821 helix: 0.08 (0.13), residues: 1474 sheet: -1.50 (0.18), residues: 763 loop : -1.84 (0.12), residues: 2584 =============================================================================== Job complete usr+sys time: 11598.53 seconds wall clock time: 209 minutes 21.08 seconds (12561.08 seconds total)