Starting phenix.real_space_refine (version: dev) on Thu Dec 15 12:38:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syk_25531/12_2022/7syk_25531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syk_25531/12_2022/7syk_25531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syk_25531/12_2022/7syk_25531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syk_25531/12_2022/7syk_25531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syk_25531/12_2022/7syk_25531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syk_25531/12_2022/7syk_25531.pdb" } resolution = 4.2 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 ASP 44": "OD1" <-> "OD2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E ASP 162": "OD1" <-> "OD2" Residue "F GLU 40": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F ASP 176": "OD1" <-> "OD2" Residue "F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "I GLU 18": "OE1" <-> "OE2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 61": "OD1" <-> "OD2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K ASP 95": "OD1" <-> "OD2" Residue "K PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 152": "OD1" <-> "OD2" Residue "K TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "M ASP 3": "OD1" <-> "OD2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 103": "OE1" <-> "OE2" Residue "O ASP 31": "OD1" <-> "OD2" Residue "O GLU 35": "OE1" <-> "OE2" Residue "O TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 25": "OE1" <-> "OE2" Residue "P PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 65": "OD1" <-> "OD2" Residue "P ASP 67": "OD1" <-> "OD2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "Q TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 101": "OD1" <-> "OD2" Residue "R GLU 102": "OE1" <-> "OE2" Residue "R ASP 116": "OD1" <-> "OD2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "T ASP 51": "OD1" <-> "OD2" Residue "T PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 45": "OE1" <-> "OE2" Residue "V ASP 90": "OD1" <-> "OD2" Residue "V GLU 113": "OE1" <-> "OE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "X ASP 9": "OD1" <-> "OD2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X GLU 114": "OE1" <-> "OE2" Residue "X PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 95": "OE1" <-> "OE2" Residue "Y ASP 98": "OD1" <-> "OD2" Residue "Y GLU 99": "OE1" <-> "OE2" Residue "Z GLU 109": "OE1" <-> "OE2" Residue "a TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "c GLU 15": "OE1" <-> "OE2" Residue "c ASP 34": "OD1" <-> "OD2" Residue "e PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 49": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 78761 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 143, 'rna2p_pyr': 111, 'rna3p_pur': 754, 'rna3p_pyr': 689} 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': 11, 'rna2p_pyr': 14, 'rna3p_pur': 73, 'rna3p_pyr': 64} Link IDs: {'rna2p': 24, 'rna3p': 137} Chain breaks: 1 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69331 SG CYS b 23 92.426 129.436 137.590 1.00 60.60 S ATOM 69352 SG CYS b 26 95.952 129.735 138.598 1.00 59.74 S ATOM 69735 SG CYS b 74 95.016 126.338 139.031 1.00 53.29 S ATOM 69754 SG CYS b 77 94.927 127.998 140.396 1.00 51.40 S ATOM 72396 SG CYS g 121 149.395 98.945 244.281 1.00244.74 S ATOM 72432 SG CYS g 126 148.469 96.439 242.787 1.00249.60 S ATOM 72550 SG CYS g 141 149.506 99.698 242.311 1.00240.65 S ATOM 72569 SG CYS g 144 145.927 99.998 242.732 1.00241.16 S Time building chain proxies: 32.76, per 1000 atoms: 0.42 Number of scatterers: 78761 At special positions: 0 Unit cell: (234.65, 193.8, 261.25, 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: 28.36 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " 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: 135 helices and 58 sheets defined 32.7% alpha, 16.2% beta 483 base pairs and 970 stacking pairs defined. Time for finding SS restraints: 21.79 Creating SS restraints... Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.820A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 36 removed outlier: 3.990A pdb=" N GLU B 35 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN B 36 " --> pdb=" O GLN B 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 32 through 36' Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 50 through 67 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 167 through 186 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.675A pdb=" N SER C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.803A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 176 removed outlier: 4.214A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 4.220A pdb=" N ASN C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 Processing helix chain 'C' and resid 224 through 232 removed outlier: 4.157A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 4.027A pdb=" N ARG D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.623A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.581A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS D 257 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 274 removed outlier: 5.831A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 109 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.757A pdb=" N ALA E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 59 through 67 Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 67 through 74 Processing helix chain 'G' and resid 85 through 105 removed outlier: 4.145A pdb=" N THR G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.967A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN G 118 " --> pdb=" O ASN G 114 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY G 120 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 183 removed outlier: 4.063A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA G 181 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 201 Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 237 removed outlier: 3.669A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 34 removed outlier: 4.280A pdb=" N SER I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 73 Processing helix chain 'I' and resid 78 through 87 Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.132A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 88 through 93 removed outlier: 3.858A pdb=" N ARG J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR J 93 " --> pdb=" O GLU J 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 88 through 93' Processing helix chain 'J' and resid 106 through 117 Processing helix chain 'J' and resid 134 through 139 Processing helix chain 'J' and resid 142 through 155 removed outlier: 3.703A pdb=" N ASN J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 192 through 207 removed outlier: 3.561A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.417A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 93 through 97 removed outlier: 3.850A pdb=" N ILE K 97 " --> pdb=" O LEU K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 108 removed outlier: 3.835A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG K 108 " --> pdb=" O ASP K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 removed outlier: 3.945A pdb=" N GLY K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 171 through 186 Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.618A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 9 " --> pdb=" O LYS L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.975A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'M' and resid 47 through 52 removed outlier: 3.903A pdb=" N ILE M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 28 Processing helix chain 'N' and resid 34 through 45 Processing helix chain 'N' and resid 60 through 70 removed outlier: 4.389A pdb=" N LEU N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 90 removed outlier: 3.646A pdb=" N GLU N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP N 88 " --> pdb=" O LYS N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 130 Processing helix chain 'O' and resid 29 through 43 removed outlier: 3.525A pdb=" N VAL O 33 " --> pdb=" O THR O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 62 through 67 removed outlier: 3.704A pdb=" N VAL O 66 " --> pdb=" O GLN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 104 Processing helix chain 'O' and resid 109 through 132 removed outlier: 3.706A pdb=" N TYR O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 89 removed outlier: 3.694A pdb=" N ALA P 74 " --> pdb=" O SER P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 122 removed outlier: 3.635A pdb=" N SER P 122 " --> pdb=" O ALA P 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 28 removed outlier: 3.697A pdb=" N MET Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.955A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 46 removed outlier: 3.595A pdb=" N ARG Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG Q 44 " --> pdb=" O ARG Q 40 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'R' and resid 47 through 63 Proline residue: R 54 - end of helix removed outlier: 7.197A pdb=" N LYS R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N GLU R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG R 62 " --> pdb=" O LEU R 58 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE R 63 " --> pdb=" O GLY R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 100 removed outlier: 3.871A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 4.266A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 removed outlier: 3.611A pdb=" N LEU R 120 " --> pdb=" O ARG R 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 117 through 120' Processing helix chain 'S' and resid 6 through 18 removed outlier: 4.037A pdb=" N LYS S 10 " --> pdb=" O THR S 6 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 39 Processing helix chain 'S' and resid 44 through 64 Processing helix chain 'S' and resid 79 through 84 removed outlier: 3.971A pdb=" N ASP S 82 " --> pdb=" O GLU S 79 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN S 83 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR S 84 " --> pdb=" O ARG S 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 79 through 84' Processing helix chain 'S' and resid 99 through 107 Processing helix chain 'T' and resid 29 through 33 removed outlier: 3.588A pdb=" N ALA T 32 " --> pdb=" O ALA T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.508A pdb=" N ALA T 41 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL T 44 " --> pdb=" O TYR T 40 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG T 46 " --> pdb=" O HIS T 42 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS T 47 " --> pdb=" O VAL T 43 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 37 through 48' Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 99 through 117 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 10 through 26 removed outlier: 4.027A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 35 removed outlier: 4.017A pdb=" N VAL U 34 " --> pdb=" O PRO U 31 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP U 35 " --> pdb=" O GLU U 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 31 through 35' Processing helix chain 'U' and resid 51 through 67 removed outlier: 4.007A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 97 through 110 Processing helix chain 'U' and resid 124 through 143 Processing helix chain 'V' and resid 29 through 46 Processing helix chain 'V' and resid 94 through 104 Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.977A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 77 removed outlier: 3.646A pdb=" N SER W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 44 Processing helix chain 'X' and resid 85 through 93 removed outlier: 3.530A pdb=" N TRP X 89 " --> pdb=" O ASP X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 120 removed outlier: 3.895A pdb=" N ARG X 118 " --> pdb=" O GLU X 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 32 through 39 removed outlier: 4.015A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 136 Processing helix chain 'Z' and resid 36 through 48 removed outlier: 4.013A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 Processing helix chain 'Z' and resid 87 through 94 removed outlier: 3.604A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 117 removed outlier: 3.705A pdb=" N ARG Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL Z 117 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 removed outlier: 4.072A pdb=" N ASN Z 124 " --> pdb=" O THR Z 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 62 Processing helix chain 'a' and resid 69 through 77 Processing helix chain 'a' and resid 80 through 95 removed outlier: 3.746A pdb=" N ALA a 84 " --> pdb=" O ARG a 80 " (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 Processing helix chain 'e' and resid 2 through 6 Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.686A pdb=" N LEU e 36 " --> pdb=" O LYS e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 46 Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 105 through 115 Processing helix chain 'g' and resid 101 through 105 Processing helix chain 'n' and resid 2 through 24 removed outlier: 3.559A pdb=" N ARG n 6 " --> pdb=" O ARG n 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41 removed outlier: 4.010A pdb=" N LYS B 40 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.641A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 47 removed outlier: 3.542A pdb=" N TYR C 31 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 13.769A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.542A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 215 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 137 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 70 removed outlier: 5.444A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 13.769A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.542A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 215 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 140 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 210 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE C 142 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.120A pdb=" N LYS D 103 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 131 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.120A pdb=" N LYS D 103 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 131 " --> pdb=" O LYS D 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.604A pdb=" N VAL D 184 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS D 188 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 225 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 36 through 39 removed outlier: 3.686A pdb=" N GLY E 36 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 38 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE E 49 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR E 87 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 155 removed outlier: 3.685A pdb=" N PHE E 152 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS E 134 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 188 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 150 through 155 removed outlier: 3.685A pdb=" N PHE E 152 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS E 134 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 175 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE E 184 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 173 " --> pdb=" O ILE E 184 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 10 removed outlier: 4.592A pdb=" N LEU F 9 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.750A pdb=" N GLU F 97 " --> pdb=" O ILE F 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.288A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.631A pdb=" N VAL F 140 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS F 122 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 162 " --> pdb=" O LYS F 122 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR F 159 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N PHE F 172 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLN F 161 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 217 through 221 removed outlier: 3.659A pdb=" N VAL F 207 " --> pdb=" O GLU F 199 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN F 197 " --> pdb=" O HIS F 209 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS F 211 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE F 195 " --> pdb=" O LYS F 211 " (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 123 through 124 removed outlier: 3.813A pdb=" N ASP G 124 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG d 44 " --> pdb=" O VAL d 30 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL d 30 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N CYS d 27 " --> pdb=" O GLY d 19 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY d 19 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.833A pdb=" N CYS H 12 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS H 2 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU H 111 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN H 4 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE H 113 " --> pdb=" O ASN H 4 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER H 6 " --> pdb=" O ILE H 113 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N LYS H 115 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.666A pdb=" N VAL H 73 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL H 97 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS H 93 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 47 through 52 removed outlier: 3.902A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL I 93 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 185 through 188 removed outlier: 4.139A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE X 52 " --> pdb=" O ILE I 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 4 Processing sheet with id=AC6, first strand: chain 'J' and resid 42 through 44 removed outlier: 6.893A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.598A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE J 101 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE J 175 " --> pdb=" O CYS J 100 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N GLY J 187 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN J 64 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL J 189 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER J 66 " --> pdb=" O VAL J 189 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 135 through 137 Processing sheet with id=AC9, first strand: chain 'L' and resid 62 through 63 Processing sheet with id=AD1, first strand: chain 'M' and resid 72 through 73 removed outlier: 7.584A pdb=" N THR M 127 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU M 143 " --> pdb=" O THR M 127 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG M 101 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 31 through 33 removed outlier: 3.875A pdb=" N VAL N 109 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL N 79 " --> pdb=" O CYS N 50 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU N 52 " --> pdb=" O VAL N 79 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 52 through 56 removed outlier: 7.371A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS P 43 " --> pdb=" O HIS P 32 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU P 93 " --> pdb=" O ILE P 126 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG P 128 " --> pdb=" O LEU P 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 75 through 77 removed outlier: 4.150A pdb=" N VAL Q 94 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN Q 98 " --> pdb=" O THR Q 101 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR Q 101 " --> pdb=" O ASN Q 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 11 through 13 removed outlier: 3.600A pdb=" N LYS R 73 " --> pdb=" O THR R 20 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS R 33 " --> pdb=" O ILE R 68 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL R 70 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 97 through 98 Processing sheet with id=AD7, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.762A pdb=" N ILE T 20 " --> pdb=" O LEU T 13 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL T 15 " --> pdb=" O THR T 18 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 81 through 83 removed outlier: 3.826A pdb=" N HIS U 91 " --> pdb=" O GLN U 83 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE1, first strand: chain 'V' and resid 59 through 66 removed outlier: 3.580A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP V 78 " --> pdb=" O THR V 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS V 85 " --> pdb=" O SER V 26 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR V 25 " --> pdb=" O GLU V 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 59 through 66 removed outlier: 3.580A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP V 78 " --> pdb=" O THR V 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS V 85 " --> pdb=" O SER V 26 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 32 through 39 removed outlier: 3.589A pdb=" N ILE W 32 " --> pdb=" O ILE W 55 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE W 55 " --> pdb=" O ILE W 32 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU W 38 " --> pdb=" O GLN W 49 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 71 through 74 removed outlier: 5.679A pdb=" N ILE X 125 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N THR X 105 " --> pdb=" O ILE X 125 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY X 127 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Y' and resid 80 through 82 removed outlier: 7.618A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU Y 52 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS Y 124 " --> pdb=" O LEU Y 101 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA Y 103 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL Y 122 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 57 through 58 Processing sheet with id=AE7, first strand: chain 'Z' and resid 6 through 15 removed outlier: 5.966A pdb=" N ILE Z 7 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU Z 28 " --> pdb=" O ILE Z 7 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N THR Z 9 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP Z 26 " --> pdb=" O THR Z 9 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LYS Z 11 " --> pdb=" O VAL Z 24 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL Z 24 " --> pdb=" O LYS Z 11 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE Z 72 " --> pdb=" O GLY Z 59 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY Z 59 " --> pdb=" O PHE Z 72 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET Z 74 " --> pdb=" O VAL Z 57 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL Z 57 " --> pdb=" O MET Z 74 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TYR Z 76 " --> pdb=" O ILE Z 55 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE Z 55 " --> pdb=" O TYR Z 76 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'a' and resid 67 through 68 removed outlier: 3.902A pdb=" N TYR a 109 " --> pdb=" O ILE a 68 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AF1, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.517A pdb=" N ILE b 36 " --> pdb=" O TYR b 73 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG b 42 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 44 through 47 removed outlier: 3.822A pdb=" N THR c 44 " --> pdb=" O VAL c 35 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'c' and resid 54 through 55 removed outlier: 6.921A pdb=" N VAL c 54 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU c 63 " --> pdb=" O VAL c 54 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'e' and resid 30 through 31 Processing sheet with id=AF5, first strand: chain 'g' and resid 133 through 134 removed outlier: 3.679A pdb=" N ALA g 133 " --> pdb=" O TYR g 140 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR g 140 " --> pdb=" O ALA g 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'h' and resid 5 through 10 removed outlier: 3.740A pdb=" N ARG h 8 " --> pdb=" O VAL h 309 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL h 309 " --> pdb=" O ARG h 8 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR h 10 " --> pdb=" O VAL h 307 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL h 307 " --> pdb=" O THR h 10 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 21 through 22 removed outlier: 3.689A pdb=" N LEU h 32 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N MET h 42 " --> pdb=" O GLN h 56 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN h 56 " --> pdb=" O MET h 42 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 66 through 71 removed outlier: 4.126A pdb=" N SER h 80 " --> pdb=" O ARG h 88 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG h 88 " --> pdb=" O SER h 80 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 110 through 113 removed outlier: 3.519A pdb=" N SER h 122 " --> pdb=" O LYS h 130 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR h 140 " --> pdb=" O LEU h 131 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 151 through 155 Processing sheet with id=AG2, first strand: chain 'h' and resid 174 through 178 removed outlier: 5.375A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 195 through 200 removed outlier: 3.553A pdb=" N THR h 199 " --> pdb=" O ALA h 208 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.251A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE h 256 " --> pdb=" O GLU h 269 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU h 269 " --> pdb=" O ILE h 256 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE h 258 " --> pdb=" O VAL h 267 " (cutoff:3.500A) 1360 hydrogen bonds defined for protein. 3897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1215 hydrogen bonds 2040 hydrogen bond angles 0 basepair planarities 483 basepair parallelities 970 stacking parallelities Total time for adding SS restraints: 59.06 Time building geometry restraints manager: 30.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14909 1.33 - 1.46: 30395 1.46 - 1.58: 34823 1.58 - 1.70: 3704 1.70 - 1.83: 274 Bond restraints: 84105 Sorted by residual: bond pdb=" CA THR R 18 " pdb=" C THR R 18 " ideal model delta sigma weight residual 1.523 1.582 -0.059 1.34e-02 5.57e+03 1.91e+01 bond pdb=" C ILE C 189 " pdb=" N PRO C 190 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.80e+00 bond pdb=" O5' G z 267 " pdb=" C5' G z 267 " ideal model delta sigma weight residual 1.420 1.452 -0.032 1.50e-02 4.44e+03 4.64e+00 bond pdb=" O3' U 21114 " pdb=" P U 21115 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.50e-02 4.44e+03 4.62e+00 bond pdb=" P G z 266 " pdb=" OP2 G z 266 " ideal model delta sigma weight residual 1.485 1.528 -0.043 2.00e-02 2.50e+03 4.61e+00 ... (remaining 84100 not shown) Histogram of bond angle deviations from ideal: 97.29 - 105.23: 9050 105.23 - 113.17: 49290 113.17 - 121.11: 40384 121.11 - 129.05: 22209 129.05 - 136.99: 1516 Bond angle restraints: 122449 Sorted by residual: angle pdb=" C LEU O 45 " pdb=" N THR O 46 " pdb=" CA THR O 46 " ideal model delta sigma weight residual 120.49 136.99 -16.50 1.42e+00 4.96e-01 1.35e+02 angle pdb=" N ILE G 33 " pdb=" CA ILE G 33 " pdb=" C ILE G 33 " ideal model delta sigma weight residual 112.29 104.93 7.36 9.40e-01 1.13e+00 6.12e+01 angle pdb=" C GLY D 175 " pdb=" N LYS D 176 " pdb=" CA LYS D 176 " ideal model delta sigma weight residual 120.49 130.26 -9.77 1.42e+00 4.96e-01 4.73e+01 angle pdb=" CA LYS T 8 " pdb=" CB LYS T 8 " pdb=" CG LYS T 8 " ideal model delta sigma weight residual 114.10 127.07 -12.97 2.00e+00 2.50e-01 4.21e+01 angle pdb=" CA ARG L 65 " pdb=" CB ARG L 65 " pdb=" CG ARG L 65 " ideal model delta sigma weight residual 114.10 126.51 -12.41 2.00e+00 2.50e-01 3.85e+01 ... (remaining 122444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 45115 35.95 - 71.90: 1612 71.90 - 107.84: 123 107.84 - 143.79: 9 143.79 - 179.74: 27 Dihedral angle restraints: 46886 sinusoidal: 32830 harmonic: 14056 Sorted by residual: dihedral pdb=" C4' G 21204 " pdb=" C3' G 21204 " pdb=" C2' G 21204 " pdb=" C1' G 21204 " ideal model delta sinusoidal sigma weight residual -35.00 30.63 -65.63 1 8.00e+00 1.56e-02 8.81e+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 -160.00 19.74 -179.74 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 21624 " pdb=" C1' U 21624 " pdb=" N1 U 21624 " pdb=" C2 U 21624 " ideal model delta sinusoidal sigma weight residual -160.00 5.40 -165.40 1 1.50e+01 4.44e-03 8.40e+01 ... (remaining 46883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 14652 0.106 - 0.213: 506 0.213 - 0.319: 31 0.319 - 0.425: 3 0.425 - 0.532: 2 Chirality restraints: 15194 Sorted by residual: chirality pdb=" CB ILE F 45 " pdb=" CA ILE F 45 " pdb=" CG1 ILE F 45 " pdb=" CG2 ILE F 45 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CB ILE I 144 " pdb=" CA ILE I 144 " pdb=" CG1 ILE I 144 " pdb=" CG2 ILE I 144 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CB VAL W 9 " pdb=" CA VAL W 9 " pdb=" CG1 VAL W 9 " pdb=" CG2 VAL W 9 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 15191 not shown) Planarity restraints: 8634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 64 " 0.058 2.00e-02 2.50e+03 4.79e-02 5.73e+01 pdb=" CG TRP L 64 " -0.127 2.00e-02 2.50e+03 pdb=" CD1 TRP L 64 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP L 64 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP L 64 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP L 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP L 64 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 64 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 64 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP L 64 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21753 " 0.041 2.00e-02 2.50e+03 2.89e-02 1.88e+01 pdb=" N1 C 21753 " -0.048 2.00e-02 2.50e+03 pdb=" C2 C 21753 " 0.043 2.00e-02 2.50e+03 pdb=" O2 C 21753 " -0.035 2.00e-02 2.50e+03 pdb=" N3 C 21753 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C 21753 " 0.011 2.00e-02 2.50e+03 pdb=" N4 C 21753 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C 21753 " -0.008 2.00e-02 2.50e+03 pdb=" C6 C 21753 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 962 " 0.040 2.00e-02 2.50e+03 1.93e-02 1.03e+01 pdb=" N9 A 2 962 " -0.049 2.00e-02 2.50e+03 pdb=" C8 A 2 962 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A 2 962 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A 2 962 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A 2 962 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A 2 962 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A 2 962 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A 2 962 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A 2 962 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A 2 962 " -0.007 2.00e-02 2.50e+03 ... (remaining 8631 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 16090 2.78 - 3.31: 64639 3.31 - 3.84: 149668 3.84 - 4.37: 171295 4.37 - 4.90: 251413 Nonbonded interactions: 653105 Sorted by model distance: nonbonded pdb=" O PHE h 65 " pdb=" OG SER h 82 " model vdw 2.255 2.440 nonbonded pdb=" O LEU C 62 " pdb=" OG1 THR C 88 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR P 45 " pdb=" O GLU P 51 " model vdw 2.269 2.440 nonbonded pdb=" O2' C 21374 " pdb=" O2 C 21464 " model vdw 2.271 2.440 nonbonded pdb=" OH TYR D 169 " pdb=" O GLY D 175 " model vdw 2.274 2.440 ... (remaining 653100 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: 3.600 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: 0.080 Extract box with map and model: 18.050 Check model and map are aligned: 0.870 Convert atoms to be neutral: 0.530 Process input model: 210.610 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 237.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 84105 Z= 0.215 Angle : 0.831 18.213 122449 Z= 0.411 Chirality : 0.043 0.532 15194 Planarity : 0.006 0.076 8634 Dihedral : 15.809 179.739 37820 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.93 % Favored : 94.05 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.72 (0.11), residues: 4821 helix: -1.71 (0.11), residues: 1465 sheet: -1.13 (0.20), residues: 680 loop : -2.07 (0.11), residues: 2676 *********************** 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 605 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 604 time to evaluate : 4.585 Fit side-chains 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: 605 average time/residue: 0.7172 time to fit residues: 744.6438 Evaluate side-chains 414 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 4.487 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4147 ------------------------------------------------------------------------------- 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: 7.9990 chunk 499 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 336 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 516 optimal weight: 30.0000 chunk 199 optimal weight: 8.9990 chunk 314 optimal weight: 9.9990 chunk 384 optimal weight: 5.9990 chunk 598 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 132 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN D 113 GLN G 79 HIS G 95 HIS H 13 GLN J 7 ASN L 50 GLN O 105 ASN S 31 ASN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 GLN U 42 HIS V 85 HIS X 24 GLN X 44 HIS a 103 HIS g 135 HIS ** h 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 84105 Z= 0.232 Angle : 0.630 9.393 122449 Z= 0.319 Chirality : 0.038 0.332 15194 Planarity : 0.005 0.060 8634 Dihedral : 15.545 179.888 27708 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.31 % Favored : 93.67 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.11), residues: 4821 helix: -0.23 (0.13), residues: 1498 sheet: -1.13 (0.19), residues: 699 loop : -1.93 (0.11), residues: 2624 *********************** 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 498 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 494 time to evaluate : 4.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 495 average time/residue: 0.7452 time to fit residues: 645.6602 Evaluate side-chains 386 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 4.485 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 332 optimal weight: 30.0000 chunk 185 optimal weight: 7.9990 chunk 498 optimal weight: 10.0000 chunk 407 optimal weight: 4.9990 chunk 165 optimal weight: 20.0000 chunk 599 optimal weight: 20.0000 chunk 647 optimal weight: 30.0000 chunk 533 optimal weight: 1.9990 chunk 594 optimal weight: 20.0000 chunk 204 optimal weight: 3.9990 chunk 480 optimal weight: 0.0070 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN D 113 GLN H 13 GLN L 50 GLN M 106 HIS O 105 ASN R 11 GLN S 31 ASN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 10 GLN V 85 HIS X 24 GLN a 103 HIS b 72 HIS c 9 HIS ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 104 HIS ** h 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 191 HIS h 215 GLN n 22 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 84105 Z= 0.174 Angle : 0.564 9.822 122449 Z= 0.286 Chirality : 0.035 0.375 15194 Planarity : 0.005 0.065 8634 Dihedral : 15.551 179.886 27708 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.99 % Favored : 93.98 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.12), residues: 4821 helix: 0.32 (0.13), residues: 1490 sheet: -1.16 (0.19), residues: 711 loop : -1.83 (0.12), residues: 2620 *********************** 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 508 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 507 time to evaluate : 4.502 Fit side-chains 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: 508 average time/residue: 0.7048 time to fit residues: 619.6464 Evaluate side-chains 388 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 4.471 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4294 ------------------------------------------------------------------------------- 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: 0.7980 chunk 450 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 286 optimal weight: 7.9990 chunk 402 optimal weight: 7.9990 chunk 601 optimal weight: 4.9990 chunk 636 optimal weight: 6.9990 chunk 314 optimal weight: 8.9990 chunk 570 optimal weight: 3.9990 chunk 171 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN C 40 ASN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN D 113 GLN F 188 ASN H 13 GLN H 65 GLN L 50 GLN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 ASN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 HIS ** W 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN Y 127 ASN a 103 HIS ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 22 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.131 84105 Z= 0.194 Angle : 0.582 10.227 122449 Z= 0.295 Chirality : 0.036 0.416 15194 Planarity : 0.005 0.056 8634 Dihedral : 15.657 179.933 27708 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.03 % Favored : 92.95 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.12), residues: 4821 helix: 0.47 (0.13), residues: 1491 sheet: -1.32 (0.19), residues: 725 loop : -1.78 (0.12), residues: 2605 *********************** 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 498 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 496 time to evaluate : 4.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 497 average time/residue: 0.7307 time to fit residues: 632.3528 Evaluate side-chains 384 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.675 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6869 ------------------------------------------------------------------------------- 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: 9.9990 chunk 361 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 474 optimal weight: 0.6980 chunk 262 optimal weight: 20.0000 chunk 543 optimal weight: 7.9990 chunk 440 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 6.9990 chunk 571 optimal weight: 5.9990 chunk 160 optimal weight: 40.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 179 ASN D 113 GLN H 13 GLN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS M 19 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN Q 98 ASN S 31 ASN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 GLN ** W 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN Y 127 ASN a 103 HIS b 25 ASN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 22 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 84105 Z= 0.262 Angle : 0.669 12.939 122449 Z= 0.338 Chirality : 0.039 0.409 15194 Planarity : 0.005 0.057 8634 Dihedral : 16.048 179.804 27708 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.99 % Favored : 91.99 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 4821 helix: 0.23 (0.13), residues: 1474 sheet: -1.56 (0.18), residues: 738 loop : -1.85 (0.12), residues: 2609 *********************** 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 476 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 475 time to evaluate : 4.571 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 475 average time/residue: 0.7246 time to fit residues: 597.7628 Evaluate side-chains 377 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 4.583 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5144 ------------------------------------------------------------------------------- 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: 5.9990 chunk 125 optimal weight: 40.0000 chunk 373 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 637 optimal weight: 0.5980 chunk 529 optimal weight: 3.9990 chunk 295 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 131 HIS ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 ASN S 31 ASN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 GLN V 85 HIS W 29 HIS W 33 GLN W 47 ASN X 24 GLN Y 127 ASN a 103 HIS ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 22 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 84105 Z= 0.154 Angle : 0.560 12.861 122449 Z= 0.284 Chirality : 0.035 0.260 15194 Planarity : 0.004 0.056 8634 Dihedral : 15.779 179.893 27708 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.68 % Favored : 94.30 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.12), residues: 4821 helix: 0.62 (0.14), residues: 1491 sheet: -1.45 (0.18), residues: 722 loop : -1.72 (0.12), residues: 2608 *********************** 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 517 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 516 time to evaluate : 4.637 Fit side-chains 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: 516 average time/residue: 0.7274 time to fit residues: 646.9118 Evaluate side-chains 391 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 4.485 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 614 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 5.9990 chunk 465 optimal weight: 30.0000 chunk 360 optimal weight: 9.9990 chunk 536 optimal weight: 7.9990 chunk 356 optimal weight: 20.0000 chunk 635 optimal weight: 0.0570 chunk 397 optimal weight: 8.9990 chunk 387 optimal weight: 0.9980 chunk 293 optimal weight: 20.0000 overall best weight: 4.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN H 81 HIS ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN Q 98 ASN ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 ASN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 HIS X 24 GLN a 103 HIS ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 22 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 84105 Z= 0.207 Angle : 0.607 12.409 122449 Z= 0.306 Chirality : 0.037 0.437 15194 Planarity : 0.005 0.057 8634 Dihedral : 15.886 179.952 27708 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.03 % Favored : 91.95 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.12), residues: 4821 helix: 0.47 (0.13), residues: 1505 sheet: -1.47 (0.18), residues: 742 loop : -1.75 (0.12), residues: 2574 *********************** 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 476 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 474 time to evaluate : 4.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 474 average time/residue: 0.7421 time to fit residues: 613.7647 Evaluate side-chains 370 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 369 time to evaluate : 4.486 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5402 time to fit residues: 6.4740 ------------------------------------------------------------------------------- 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: 0.8980 chunk 253 optimal weight: 0.2980 chunk 379 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 124 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 403 optimal weight: 6.9990 chunk 432 optimal weight: 20.0000 chunk 314 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 499 optimal weight: 20.0000 overall best weight: 5.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN H 65 GLN ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 ASN S 31 ASN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 GLN V 85 HIS X 24 GLN Y 61 GLN a 103 HIS d 45 ASN ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 22 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.104 84105 Z= 0.213 Angle : 0.614 14.876 122449 Z= 0.310 Chirality : 0.037 0.273 15194 Planarity : 0.005 0.070 8634 Dihedral : 15.957 179.773 27708 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.51 % Favored : 92.47 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.12), residues: 4821 helix: 0.47 (0.13), residues: 1499 sheet: -1.42 (0.18), residues: 734 loop : -1.79 (0.12), residues: 2588 *********************** 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 473 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 472 time to evaluate : 4.672 Fit side-chains 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: 472 average time/residue: 0.7357 time to fit residues: 602.8928 Evaluate side-chains 376 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 4.484 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4012 ------------------------------------------------------------------------------- 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: 9.9990 chunk 608 optimal weight: 0.0970 chunk 555 optimal weight: 2.9990 chunk 591 optimal weight: 5.9990 chunk 356 optimal weight: 30.0000 chunk 257 optimal weight: 10.0000 chunk 464 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 534 optimal weight: 5.9990 chunk 559 optimal weight: 7.9990 chunk 589 optimal weight: 9.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 ASN ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN S 31 ASN ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 GLN V 85 HIS X 24 GLN a 103 HIS d 45 ASN ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 22 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 84105 Z= 0.190 Angle : 0.593 14.784 122449 Z= 0.299 Chirality : 0.036 0.288 15194 Planarity : 0.005 0.061 8634 Dihedral : 15.920 179.642 27708 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.90 % Favored : 92.08 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.12), residues: 4821 helix: 0.55 (0.13), residues: 1491 sheet: -1.47 (0.18), residues: 759 loop : -1.75 (0.12), residues: 2571 *********************** 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 474 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 472 time to evaluate : 4.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 472 average time/residue: 0.7851 time to fit residues: 646.1276 Evaluate side-chains 374 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 373 time to evaluate : 4.669 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5709 time to fit residues: 6.7187 ------------------------------------------------------------------------------- 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: 1.9990 chunk 625 optimal weight: 3.9990 chunk 382 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 435 optimal weight: 20.0000 chunk 656 optimal weight: 30.0000 chunk 604 optimal weight: 4.9990 chunk 522 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 403 optimal weight: 0.2980 chunk 320 optimal weight: 6.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN D 115 GLN E 22 ASN ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS O 105 ASN Q 98 ASN R 11 GLN S 31 ASN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 GLN V 85 HIS X 24 GLN a 103 HIS d 45 ASN ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 22 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 84105 Z= 0.151 Angle : 0.557 14.501 122449 Z= 0.281 Chirality : 0.035 0.255 15194 Planarity : 0.004 0.055 8634 Dihedral : 15.752 179.365 27708 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.43 % Favored : 93.55 % 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: -1.31 (0.12), residues: 4821 helix: 0.64 (0.14), residues: 1485 sheet: -1.34 (0.18), residues: 748 loop : -1.67 (0.12), residues: 2588 ********************** 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 487 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 486 time to evaluate : 5.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 486 average time/residue: 0.7580 time to fit residues: 637.7339 Evaluate side-chains 374 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 4.523 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7215 ------------------------------------------------------------------------------- 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: 6.9990 chunk 556 optimal weight: 10.0000 chunk 160 optimal weight: 40.0000 chunk 482 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 30.0000 chunk 523 optimal weight: 6.9990 chunk 219 optimal weight: 20.0000 chunk 537 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 overall best weight: 5.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN E 22 ASN H 65 GLN ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 ASN R 11 GLN S 29 HIS S 31 ASN ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 HIS W 2 GLN X 24 GLN a 103 HIS d 45 ASN ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 22 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.078678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.064684 restraints weight = 451870.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.065188 restraints weight = 296708.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.065315 restraints weight = 193186.060| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 84105 Z= 0.239 Angle : 0.644 16.104 122449 Z= 0.324 Chirality : 0.038 0.260 15194 Planarity : 0.005 0.061 8634 Dihedral : 16.006 179.871 27708 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.09 % Favored : 90.89 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.12), residues: 4821 helix: 0.41 (0.13), residues: 1485 sheet: -1.51 (0.18), residues: 764 loop : -1.75 (0.12), residues: 2572 =============================================================================== Job complete usr+sys time: 10905.11 seconds wall clock time: 197 minutes 41.70 seconds (11861.70 seconds total)