Starting phenix.real_space_refine on Thu Dec 14 05:04:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtu_32801/12_2023/7wtu_32801_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtu_32801/12_2023/7wtu_32801.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtu_32801/12_2023/7wtu_32801_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtu_32801/12_2023/7wtu_32801_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtu_32801/12_2023/7wtu_32801_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtu_32801/12_2023/7wtu_32801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtu_32801/12_2023/7wtu_32801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtu_32801/12_2023/7wtu_32801_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtu_32801/12_2023/7wtu_32801_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1575 5.49 5 S 219 5.16 5 C 45230 2.51 5 N 14847 2.21 5 O 19343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 81215 Number of models: 1 Model: "" Number of chains: 35 Chain: "2" Number of atoms: 33634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1575, 33634 Classifications: {'RNA': 1575} Modifications used: {'rna2p': 1, 'rna2p_pur': 120, 'rna2p_pyr': 95, 'rna3p_pur': 714, 'rna3p_pyr': 645} Link IDs: {'rna2p': 215, 'rna3p': 1359} Chain breaks: 18 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 673 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 78} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "B" 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: "c" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 471 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" 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: "e" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 179 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "F" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1494 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "x" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1372 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "X" 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: "w" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2610 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 16, 'TRANS': 314} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "W" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "u" Number of atoms: 5168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5168 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 597} Chain breaks: 5 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "t" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 520 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain breaks: 2 Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "S" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1054 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "Q" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1006 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain breaks: 1 Chain: "O" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1009 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" 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: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "r" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 940 Classifications: {'peptide': 118} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 106} Chain: "q" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1869 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 13, 'TRANS': 221} Chain breaks: 1 Chain: "K" Number of atoms: 7949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7949 Classifications: {'peptide': 1022} Link IDs: {'CIS': 1, 'PTRANS': 49, 'TRANS': 971} Chain breaks: 10 Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 2 Chain: "f" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 465 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain breaks: 1 Chain: "z" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 679 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain breaks: 1 Chain: "q" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "f" 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 80297 SG CYS f 121 192.125 132.703 29.164 1.00 18.47 S ATOM 80333 SG CYS f 126 191.275 132.728 33.243 1.00 19.34 S ATOM 80451 SG CYS f 141 189.122 134.551 30.338 1.00 21.50 S Time building chain proxies: 31.76, per 1000 atoms: 0.39 Number of scatterers: 81215 At special positions: 0 Unit cell: (255.219, 254.16, 202.269, 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 1 29.99 S 219 16.00 P 1575 15.00 O 19343 8.00 N 14847 7.00 C 45230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.31 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 121 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 126 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 141 " 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11174 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 234 helices and 47 sheets defined 41.5% alpha, 11.8% beta 511 base pairs and 893 stacking pairs defined. Time for finding SS restraints: 33.82 Creating SS restraints... Processing helix chain 'R' and resid 8 through 23 removed outlier: 7.644A pdb=" N THR R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 38 Processing helix chain 'R' and resid 44 through 63 removed outlier: 3.627A pdb=" N GLN R 62 " --> pdb=" O MET R 58 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 82 Processing helix chain 'b' and resid 12 through 17 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 158 through 177 Processing helix chain 'B' and resid 181 through 190 Proline residue: B 190 - end of helix Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 58 through 67 removed outlier: 3.672A pdb=" N GLN E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 248 through 261 Processing helix chain 'e' and resid 31 through 41 Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 68 through 76 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 86 through 104 Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 143 through 161 Processing helix chain 'F' and resid 169 through 182 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'H' and resid 18 through 33 Processing helix chain 'H' and resid 37 through 40 No H-bonds generated for 'chain 'H' and resid 37 through 40' Processing helix chain 'H' and resid 66 through 74 removed outlier: 5.372A pdb=" N LYS H 70 " --> pdb=" O PRO H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 86 Processing helix chain 'H' and resid 118 through 120 No H-bonds generated for 'chain 'H' and resid 118 through 120' Processing helix chain 'H' and resid 122 through 132 Processing helix chain 'H' and resid 167 through 181 removed outlier: 3.863A pdb=" N VAL H 170 " --> pdb=" O GLU H 167 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU H 171 " --> pdb=" O HIS H 168 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 172 " --> pdb=" O LYS H 169 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR H 181 " --> pdb=" O LYS H 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 24 No H-bonds generated for 'chain 'G' and resid 21 through 24' Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'G' and resid 154 through 156 No H-bonds generated for 'chain 'G' and resid 154 through 156' Processing helix chain 'G' and resid 182 through 228 Processing helix chain 'Z' and resid 52 through 61 Processing helix chain 'Z' and resid 70 through 77 Processing helix chain 'Z' and resid 81 through 93 Processing helix chain 'Y' and resid 37 through 48 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 79 through 85 Processing helix chain 'Y' and resid 88 through 92 Processing helix chain 'Y' and resid 104 through 116 removed outlier: 3.511A pdb=" N LYS Y 115 " --> pdb=" O LYS Y 111 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS Y 116 " --> pdb=" O ASN Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 124 Processing helix chain 'x' and resid 85 through 90 Processing helix chain 'x' and resid 93 through 100 Proline residue: x 98 - end of helix Processing helix chain 'x' and resid 127 through 142 Processing helix chain 'x' and resid 146 through 154 Processing helix chain 'x' and resid 174 through 184 Processing helix chain 'x' and resid 186 through 198 removed outlier: 6.181A pdb=" N THR x 190 " --> pdb=" O GLY x 187 " (cutoff:3.500A) Processing helix chain 'x' and resid 215 through 230 Processing helix chain 'x' and resid 234 through 246 removed outlier: 4.603A pdb=" N SER x 246 " --> pdb=" O ARG x 242 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 22 Processing helix chain 'X' and resid 25 through 32 Processing helix chain 'X' and resid 34 through 38 Processing helix chain 'X' and resid 90 through 93 Processing helix chain 'X' and resid 130 through 134 Processing helix chain 'w' and resid 19 through 27 Processing helix chain 'w' and resid 52 through 71 Processing helix chain 'w' and resid 143 through 166 Processing helix chain 'w' and resid 181 through 194 removed outlier: 4.043A pdb=" N LYS w 194 " --> pdb=" O GLU w 190 " (cutoff:3.500A) Processing helix chain 'w' and resid 207 through 209 No H-bonds generated for 'chain 'w' and resid 207 through 209' Processing helix chain 'w' and resid 213 through 219 Processing helix chain 'w' and resid 227 through 239 Processing helix chain 'w' and resid 244 through 252 Processing helix chain 'w' and resid 254 through 265 Processing helix chain 'w' and resid 270 through 280 Processing helix chain 'w' and resid 283 through 289 Processing helix chain 'w' and resid 291 through 295 Processing helix chain 'w' and resid 302 through 314 Processing helix chain 'w' and resid 319 through 331 Processing helix chain 'w' and resid 338 through 347 Processing helix chain 'w' and resid 354 through 366 Processing helix chain 'w' and resid 376 through 388 Processing helix chain 'w' and resid 395 through 407 Processing helix chain 'w' and resid 414 through 422 Processing helix chain 'W' and resid 6 through 19 Processing helix chain 'W' and resid 32 through 44 removed outlier: 3.620A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 93 Processing helix chain 'W' and resid 113 through 118 Processing helix chain 'u' and resid 50 through 74 Processing helix chain 'u' and resid 96 through 102 Processing helix chain 'u' and resid 143 through 151 Processing helix chain 'u' and resid 168 through 180 Processing helix chain 'u' and resid 197 through 212 removed outlier: 4.500A pdb=" N ILE u 201 " --> pdb=" O LEU u 197 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP u 202 " --> pdb=" O LYS u 198 " (cutoff:3.500A) Processing helix chain 'u' and resid 226 through 237 Processing helix chain 'u' and resid 245 through 248 No H-bonds generated for 'chain 'u' and resid 245 through 248' Processing helix chain 'u' and resid 401 through 403 No H-bonds generated for 'chain 'u' and resid 401 through 403' Processing helix chain 'u' and resid 465 through 483 Processing helix chain 'u' and resid 496 through 499 No H-bonds generated for 'chain 'u' and resid 496 through 499' Processing helix chain 'u' and resid 523 through 525 No H-bonds generated for 'chain 'u' and resid 523 through 525' Processing helix chain 'u' and resid 533 through 546 Processing helix chain 'u' and resid 567 through 575 Processing helix chain 'u' and resid 721 through 725 Processing helix chain 't' and resid 264 through 267 No H-bonds generated for 'chain 't' and resid 264 through 267' Processing helix chain 't' and resid 292 through 301 Processing helix chain 't' and resid 352 through 356 Processing helix chain 'T' and resid 6 through 8 No H-bonds generated for 'chain 'T' and resid 6 through 8' Processing helix chain 'T' and resid 11 through 25 Processing helix chain 'T' and resid 32 through 34 No H-bonds generated for 'chain 'T' and resid 32 through 34' Processing helix chain 'T' and resid 52 through 66 Processing helix chain 'T' and resid 72 through 78 Processing helix chain 'T' and resid 97 through 109 Processing helix chain 'T' and resid 125 through 142 Processing helix chain 'S' and resid 26 through 29 No H-bonds generated for 'chain 'S' and resid 26 through 29' Processing helix chain 'S' and resid 38 through 47 Processing helix chain 'S' and resid 61 through 72 Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 81 through 83 No H-bonds generated for 'chain 'S' and resid 81 through 83' Processing helix chain 'S' and resid 102 through 116 Processing helix chain 'S' and resid 120 through 127 Processing helix chain 'Q' and resid 48 through 51 No H-bonds generated for 'chain 'Q' and resid 48 through 51' Processing helix chain 'Q' and resid 53 through 58 Processing helix chain 'Q' and resid 77 through 98 Processing helix chain 'Q' and resid 102 through 115 Processing helix chain 'Q' and resid 117 through 119 No H-bonds generated for 'chain 'Q' and resid 117 through 119' Processing helix chain 'P' and resid 22 through 26 Processing helix chain 'P' and resid 33 through 35 No H-bonds generated for 'chain 'P' and resid 33 through 35' Processing helix chain 'P' and resid 39 through 47 Processing helix chain 'P' and resid 51 through 65 Processing helix chain 'P' and resid 87 through 89 No H-bonds generated for 'chain 'P' and resid 87 through 89' Processing helix chain 'P' and resid 109 through 111 No H-bonds generated for 'chain 'P' and resid 109 through 111' Processing helix chain 'P' and resid 117 through 119 No H-bonds generated for 'chain 'P' and resid 117 through 119' Processing helix chain 'O' and resid 58 through 61 No H-bonds generated for 'chain 'O' and resid 58 through 61' Processing helix chain 'O' and resid 71 through 88 Processing helix chain 'O' and resid 110 through 121 Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 47 through 56 Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 77 Processing helix chain 'N' and resid 86 through 104 Processing helix chain 'N' and resid 109 through 131 Processing helix chain 'N' and resid 147 through 149 No H-bonds generated for 'chain 'N' and resid 147 through 149' Processing helix chain 'L' and resid 24 through 29 Processing helix chain 'L' and resid 48 through 51 No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 40 through 62 Processing helix chain 'J' and resid 68 through 83 Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 94 through 99 removed outlier: 4.169A pdb=" N LEU J 98 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY J 99 " --> pdb=" O ASP J 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 94 through 99' Processing helix chain 'J' and resid 102 through 107 Processing helix chain 'J' and resid 110 through 116 Processing helix chain 'J' and resid 123 through 131 Processing helix chain 'J' and resid 172 through 178 Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'I' and resid 107 through 116 Processing helix chain 'I' and resid 131 through 137 Processing helix chain 'I' and resid 143 through 155 removed outlier: 4.484A pdb=" N ASN I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 168 Processing helix chain 'I' and resid 179 through 182 No H-bonds generated for 'chain 'I' and resid 179 through 182' Processing helix chain 'I' and resid 192 through 205 Processing helix chain 'r' and resid 3 through 7 Processing helix chain 'r' and resid 39 through 46 Processing helix chain 'r' and resid 51 through 60 Processing helix chain 'r' and resid 78 through 89 Processing helix chain 'q' and resid 8 through 11 No H-bonds generated for 'chain 'q' and resid 8 through 11' Processing helix chain 'q' and resid 14 through 17 No H-bonds generated for 'chain 'q' and resid 14 through 17' Processing helix chain 'q' and resid 20 through 28 Processing helix chain 'q' and resid 30 through 46 Processing helix chain 'q' and resid 66 through 74 Processing helix chain 'q' and resid 85 through 93 Processing helix chain 'q' and resid 126 through 129 removed outlier: 3.675A pdb=" N CYS q 129 " --> pdb=" O GLN q 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 126 through 129' Processing helix chain 'q' and resid 138 through 152 Processing helix chain 'q' and resid 168 through 179 Processing helix chain 'q' and resid 250 through 262 Processing helix chain 'K' and resid 110 through 114 Processing helix chain 'K' and resid 118 through 121 No H-bonds generated for 'chain 'K' and resid 118 through 121' Processing helix chain 'K' and resid 130 through 133 No H-bonds generated for 'chain 'K' and resid 130 through 133' Processing helix chain 'K' and resid 138 through 140 No H-bonds generated for 'chain 'K' and resid 138 through 140' Processing helix chain 'K' and resid 146 through 155 removed outlier: 3.669A pdb=" N MET K 152 " --> pdb=" O PHE K 148 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N THR K 153 " --> pdb=" O ALA K 149 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR K 154 " --> pdb=" O ALA K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 176 removed outlier: 4.209A pdb=" N LYS K 176 " --> pdb=" O ASN K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 204 removed outlier: 5.475A pdb=" N SER K 188 " --> pdb=" O ILE K 184 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ASP K 189 " --> pdb=" O LYS K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 223 Processing helix chain 'K' and resid 233 through 244 removed outlier: 3.947A pdb=" N PHE K 244 " --> pdb=" O GLY K 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 264 Processing helix chain 'K' and resid 281 through 294 Processing helix chain 'K' and resid 303 through 314 Processing helix chain 'K' and resid 320 through 334 Processing helix chain 'K' and resid 339 through 354 Processing helix chain 'K' and resid 364 through 376 removed outlier: 3.608A pdb=" N TYR K 375 " --> pdb=" O ILE K 371 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP K 376 " --> pdb=" O THR K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 404 Processing helix chain 'K' and resid 406 through 425 Proline residue: K 414 - end of helix removed outlier: 4.213A pdb=" N LEU K 425 " --> pdb=" O VAL K 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 445 Processing helix chain 'K' and resid 451 through 454 No H-bonds generated for 'chain 'K' and resid 451 through 454' Processing helix chain 'K' and resid 464 through 479 removed outlier: 3.924A pdb=" N LEU K 479 " --> pdb=" O VAL K 475 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 505 removed outlier: 6.393A pdb=" N ARG K 503 " --> pdb=" O GLU K 499 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLN K 504 " --> pdb=" O ALA K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 511 through 521 removed outlier: 3.901A pdb=" N LEU K 521 " --> pdb=" O CYS K 517 " (cutoff:3.500A) Processing helix chain 'K' and resid 528 through 542 Processing helix chain 'K' and resid 544 through 550 Processing helix chain 'K' and resid 568 through 576 Processing helix chain 'K' and resid 582 through 605 Proline residue: K 591 - end of helix Processing helix chain 'K' and resid 611 through 622 Processing helix chain 'K' and resid 625 through 629 Processing helix chain 'K' and resid 636 through 642 removed outlier: 3.589A pdb=" N PHE K 640 " --> pdb=" O VAL K 636 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS K 641 " --> pdb=" O ALA K 637 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLY K 642 " --> pdb=" O ILE K 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 636 through 642' Processing helix chain 'K' and resid 644 through 652 Processing helix chain 'K' and resid 655 through 671 removed outlier: 4.562A pdb=" N VAL K 659 " --> pdb=" O PRO K 655 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N THR K 660 " --> pdb=" O ASP K 656 " (cutoff:3.500A) Processing helix chain 'K' and resid 676 through 697 removed outlier: 4.452A pdb=" N ASN K 688 " --> pdb=" O ARG K 684 " (cutoff:3.500A) Proline residue: K 691 - end of helix Processing helix chain 'K' and resid 710 through 722 Processing helix chain 'K' and resid 726 through 741 Processing helix chain 'K' and resid 747 through 761 Processing helix chain 'K' and resid 766 through 781 Proline residue: K 778 - end of helix removed outlier: 4.881A pdb=" N GLU K 781 " --> pdb=" O ARG K 777 " (cutoff:3.500A) Processing helix chain 'K' and resid 785 through 798 Processing helix chain 'K' and resid 805 through 812 Processing helix chain 'K' and resid 814 through 823 Processing helix chain 'K' and resid 831 through 843 Proline residue: K 835 - end of helix Processing helix chain 'K' and resid 852 through 866 Proline residue: K 860 - end of helix Processing helix chain 'K' and resid 871 through 889 Processing helix chain 'K' and resid 895 through 904 Processing helix chain 'K' and resid 907 through 910 Processing helix chain 'K' and resid 914 through 928 Processing helix chain 'K' and resid 937 through 952 removed outlier: 3.690A pdb=" N ALA K 952 " --> pdb=" O CYS K 948 " (cutoff:3.500A) Processing helix chain 'K' and resid 956 through 972 Processing helix chain 'K' and resid 975 through 990 removed outlier: 4.308A pdb=" N LYS K 980 " --> pdb=" O ALA K 976 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS K 981 " --> pdb=" O HIS K 977 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLN K 983 " --> pdb=" O ALA K 979 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU K 984 " --> pdb=" O LYS K 980 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL K 985 " --> pdb=" O HIS K 981 " (cutoff:3.500A) Processing helix chain 'K' and resid 995 through 999 Processing helix chain 'K' and resid 1001 through 1014 Processing helix chain 'K' and resid 1017 through 1023 Processing helix chain 'K' and resid 1026 through 1041 removed outlier: 3.967A pdb=" N ARG K1030 " --> pdb=" O GLU K1026 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL K1031 " --> pdb=" O GLU K1027 " (cutoff:3.500A) Processing helix chain 'K' and resid 1073 through 1076 No H-bonds generated for 'chain 'K' and resid 1073 through 1076' Processing helix chain 'K' and resid 1126 through 1128 No H-bonds generated for 'chain 'K' and resid 1126 through 1128' Processing helix chain 'K' and resid 1189 through 1214 Proline residue: K1209 - end of helix Processing helix chain 'M' and resid 15 through 28 removed outlier: 4.021A pdb=" N GLU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 42 Processing helix chain 'M' and resid 64 through 71 Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 120 through 128 Processing helix chain 'z' and resid 104 through 129 removed outlier: 3.532A pdb=" N HIS z 129 " --> pdb=" O ALA z 125 " (cutoff:3.500A) Processing helix chain 'z' and resid 183 through 201 Processing helix chain 'z' and resid 205 through 207 No H-bonds generated for 'chain 'z' and resid 205 through 207' Processing helix chain 'z' and resid 210 through 224 Processing sheet with id= A, first strand: chain 'b' and resid 43 through 47 Processing sheet with id= B, first strand: chain 'B' and resid 65 through 70 removed outlier: 5.132A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 120 through 127 removed outlier: 3.729A pdb=" N ARG B 136 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL B 212 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 28 through 34 Processing sheet with id= E, first strand: chain 'c' and resid 55 through 58 removed outlier: 6.924A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'c' and resid 19 through 21 Processing sheet with id= G, first strand: chain 'E' and resid 70 through 72 removed outlier: 4.248A pdb=" N HIS E 112 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 121 through 125 removed outlier: 6.503A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 146 through 148 Processing sheet with id= J, first strand: chain 'E' and resid 225 through 229 removed outlier: 6.887A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 123 through 129 Processing sheet with id= L, first strand: chain 'H' and resid 47 through 53 Processing sheet with id= M, first strand: chain 'H' and resid 141 through 146 Processing sheet with id= N, first strand: chain 'G' and resid 12 through 17 removed outlier: 7.084A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 72 through 77 Processing sheet with id= P, first strand: chain 'G' and resid 160 through 162 Processing sheet with id= Q, first strand: chain 'G' and resid 54 through 57 Processing sheet with id= R, first strand: chain 'Z' and resid 97 through 101 removed outlier: 7.090A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Y' and resid 6 through 9 Processing sheet with id= T, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id= U, first strand: chain 'x' and resid 75 through 79 Processing sheet with id= V, first strand: chain 'x' and resid 159 through 164 Processing sheet with id= W, first strand: chain 'X' and resid 80 through 84 removed outlier: 6.333A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA X 103 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL X 122 " --> pdb=" O ALA X 103 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= Y, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.403A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'u' and resid 220 through 222 removed outlier: 9.451A pdb=" N LEU u 221 " --> pdb=" O TYR u 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU u 187 " --> pdb=" O LEU u 221 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'u' and resid 252 through 254 Processing sheet with id= AB, first strand: chain 'u' and resid 257 through 264 removed outlier: 3.614A pdb=" N SER u 263 " --> pdb=" O VAL u 269 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'u' and resid 628 through 631 removed outlier: 6.108A pdb=" N VAL u 597 " --> pdb=" O LEU u 684 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU u 684 " --> pdb=" O VAL u 597 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ARG u 599 " --> pdb=" O GLY u 682 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLY u 682 " --> pdb=" O ARG u 599 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'u' and resid 621 through 626 removed outlier: 9.309A pdb=" N GLU u 613 " --> pdb=" O GLN u 670 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN u 670 " --> pdb=" O GLU u 613 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS u 669 " --> pdb=" O LEU u 678 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU u 678 " --> pdb=" O LYS u 669 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'u' and resid 731 through 733 removed outlier: 6.810A pdb=" N VAL u 712 " --> pdb=" O PHE u 704 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE u 706 " --> pdb=" O MET u 710 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N MET u 710 " --> pdb=" O ILE u 706 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER u 754 " --> pdb=" O ILE u 741 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE u 741 " --> pdb=" O SER u 754 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'T' and resid 81 through 83 Processing sheet with id= AG, first strand: chain 'T' and resid 113 through 115 Processing sheet with id= AH, first strand: chain 'S' and resid 12 through 15 Processing sheet with id= AI, first strand: chain 'Q' and resid 9 through 15 Processing sheet with id= AJ, first strand: chain 'P' and resid 75 through 78 removed outlier: 6.528A pdb=" N MET P 93 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR P 78 " --> pdb=" O MET P 93 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY P 95 " --> pdb=" O THR P 78 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.483A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA O 92 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N CYS O 31 " --> pdb=" O ALA O 92 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N HIS O 94 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE O 33 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS O 96 " --> pdb=" O ILE O 33 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA O 35 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG O 98 " --> pdb=" O ALA O 35 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'L' and resid 125 through 129 removed outlier: 17.821A pdb=" N ILE L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.269A pdb=" N LEU L 93 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N SER L 74 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP L 91 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL L 87 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG L 139 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N HIS L 112 " --> pdb=" O ARG L 139 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN L 141 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 62 through 67 Processing sheet with id= AN, first strand: chain 'I' and resid 187 through 189 removed outlier: 6.205A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 42 through 47 removed outlier: 6.524A pdb=" N HIS I 44 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ALA I 57 " --> pdb=" O HIS I 44 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL I 46 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR I 55 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'r' and resid 106 through 110 removed outlier: 6.965A pdb=" N GLU r 29 " --> pdb=" O ILE r 94 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'q' and resid 56 through 59 removed outlier: 6.558A pdb=" N TYR q 77 " --> pdb=" O LEU q 57 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASP q 59 " --> pdb=" O TYR q 77 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL q 79 " --> pdb=" O ASP q 59 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'q' and resid 119 through 122 Processing sheet with id= AS, first strand: chain 'q' and resid 188 through 190 Processing sheet with id= AT, first strand: chain 'M' and resid 31 through 33 removed outlier: 6.532A pdb=" N ASN M 75 " --> pdb=" O CYS M 50 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU M 52 " --> pdb=" O ASN M 75 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE M 77 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'f' and resid 133 through 135 1923 hydrogen bonds defined for protein. 5448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1260 hydrogen bonds 1932 hydrogen bond angles 0 basepair planarities 511 basepair parallelities 893 stacking parallelities Total time for adding SS restraints: 67.59 Time building geometry restraints manager: 35.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 10017 1.31 - 1.44: 31565 1.44 - 1.57: 40968 1.57 - 1.70: 3133 1.70 - 1.82: 339 Bond restraints: 86022 Sorted by residual: bond pdb=" C4' G7M 21639 " pdb=" C3' G7M 21639 " ideal model delta sigma weight residual 1.527 1.271 0.256 1.50e-02 4.44e+03 2.92e+02 bond pdb=" C2' G7M 21639 " pdb=" C1' G7M 21639 " ideal model delta sigma weight residual 1.526 1.275 0.251 1.50e-02 4.44e+03 2.80e+02 bond pdb=" C3' G7M 21639 " pdb=" C2' G7M 21639 " ideal model delta sigma weight residual 1.525 1.674 -0.149 1.50e-02 4.44e+03 9.90e+01 bond pdb=" O4' G7M 21639 " pdb=" C1' G7M 21639 " ideal model delta sigma weight residual 1.415 1.533 -0.118 1.50e-02 4.44e+03 6.23e+01 bond pdb=" C4' G7M 21639 " pdb=" O4' G7M 21639 " ideal model delta sigma weight residual 1.454 1.560 -0.106 1.50e-02 4.44e+03 5.02e+01 ... (remaining 86017 not shown) Histogram of bond angle deviations from ideal: 96.78 - 104.61: 7485 104.61 - 112.43: 46869 112.43 - 120.25: 36839 120.25 - 128.08: 29648 128.08 - 135.90: 2791 Bond angle restraints: 123632 Sorted by residual: angle pdb=" C ILE w 206 " pdb=" N ILE w 207 " pdb=" CA ILE w 207 " ideal model delta sigma weight residual 120.24 124.24 -4.00 6.30e-01 2.52e+00 4.03e+01 angle pdb=" C VAL u 773 " pdb=" N PHE u 774 " pdb=" CA PHE u 774 " ideal model delta sigma weight residual 122.90 135.90 -13.00 2.07e+00 2.33e-01 3.94e+01 angle pdb=" CA GLY q 118 " pdb=" C GLY q 118 " pdb=" O GLY q 118 " ideal model delta sigma weight residual 122.22 118.18 4.04 6.50e-01 2.37e+00 3.86e+01 angle pdb=" C4' A 2 102 " pdb=" C3' A 2 102 " pdb=" O3' A 2 102 " ideal model delta sigma weight residual 109.40 116.96 -7.56 1.50e+00 4.44e-01 2.54e+01 angle pdb=" N HIS K 506 " pdb=" CA HIS K 506 " pdb=" C HIS K 506 " ideal model delta sigma weight residual 109.81 120.60 -10.79 2.21e+00 2.05e-01 2.38e+01 ... (remaining 123627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 49064 35.84 - 71.68: 3498 71.68 - 107.53: 495 107.53 - 143.37: 17 143.37 - 179.21: 26 Dihedral angle restraints: 53100 sinusoidal: 35870 harmonic: 17230 Sorted by residual: dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 15.00 -175.00 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 2 427 " pdb=" C1' U 2 427 " pdb=" N1 U 2 427 " pdb=" C2 U 2 427 " ideal model delta sinusoidal sigma weight residual -160.00 12.64 -172.64 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U 2 823 " pdb=" C1' U 2 823 " pdb=" N1 U 2 823 " pdb=" C2 U 2 823 " ideal model delta sinusoidal sigma weight residual -160.00 4.42 -164.42 1 1.50e+01 4.44e-03 8.38e+01 ... (remaining 53097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 13315 0.073 - 0.146: 1601 0.146 - 0.220: 169 0.220 - 0.293: 41 0.293 - 0.366: 9 Chirality restraints: 15135 Sorted by residual: chirality pdb=" C3' G 2 114 " pdb=" C4' G 2 114 " pdb=" O3' G 2 114 " pdb=" C2' G 2 114 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C1' G 21872 " pdb=" O4' G 21872 " pdb=" C2' G 21872 " pdb=" N9 G 21872 " both_signs ideal model delta sigma weight residual False 2.46 2.12 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C3' U 2 314 " pdb=" C4' U 2 314 " pdb=" O3' U 2 314 " pdb=" C2' U 2 314 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 15132 not shown) Planarity restraints: 9840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' G7M 21639 " -0.785 2.00e-02 2.50e+03 5.24e-01 6.17e+03 pdb=" C4' G7M 21639 " 0.274 2.00e-02 2.50e+03 pdb=" O4' G7M 21639 " 0.643 2.00e-02 2.50e+03 pdb=" C3' G7M 21639 " -0.200 2.00e-02 2.50e+03 pdb=" O3' G7M 21639 " 0.760 2.00e-02 2.50e+03 pdb=" C2' G7M 21639 " -0.549 2.00e-02 2.50e+03 pdb=" O2' G7M 21639 " -0.539 2.00e-02 2.50e+03 pdb=" C1' G7M 21639 " 0.392 2.00e-02 2.50e+03 pdb=" N9 G7M 21639 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 23 " 0.032 2.00e-02 2.50e+03 2.72e-02 1.85e+01 pdb=" CG TRP F 23 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP F 23 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP F 23 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 23 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 23 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 23 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 23 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP w 225 " -0.029 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP w 225 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP w 225 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP w 225 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP w 225 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP w 225 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP w 225 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP w 225 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP w 225 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP w 225 " 0.001 2.00e-02 2.50e+03 ... (remaining 9837 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 1677 2.64 - 3.20: 65155 3.20 - 3.77: 148047 3.77 - 4.33: 199074 4.33 - 4.90: 284841 Nonbonded interactions: 698794 Sorted by model distance: nonbonded pdb=" O4 U 2 749 " pdb=" O6 G 2 793 " model vdw 2.075 3.040 nonbonded pdb=" OG1 THR E 247 " pdb=" OE1 GLU E 250 " model vdw 2.131 2.440 nonbonded pdb=" O2 U 2 885 " pdb=" O6 G 2 901 " model vdw 2.172 2.432 nonbonded pdb=" OP1 A 2 634 " pdb=" OH TYR X 134 " model vdw 2.190 2.440 nonbonded pdb=" N4 C 2 748 " pdb=" N6 A 2 794 " model vdw 2.196 3.200 ... (remaining 698789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 12.380 Check model and map are aligned: 0.880 Set scattering table: 0.580 Process input model: 239.830 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 270.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 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 : 0.006 0.256 86022 Z= 0.358 Angle : 0.904 14.578 123632 Z= 0.481 Chirality : 0.049 0.366 15135 Planarity : 0.009 0.524 9840 Dihedral : 20.714 179.209 41926 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.33 % Favored : 95.65 % Rotamer: Outliers : 0.86 % Allowed : 0.80 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.05 % Twisted Proline : 0.78 % Twisted General : 0.09 % 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: -1.34 (0.10), residues: 5838 helix: -0.50 (0.09), residues: 2574 sheet: -0.64 (0.18), residues: 815 loop : -1.27 (0.11), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP F 23 HIS 0.022 0.002 HIS u 617 PHE 0.040 0.003 PHE J 147 TYR 0.037 0.002 TYR I 109 ARG 0.016 0.001 ARG c 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 677 time to evaluate : 5.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 6 residues processed: 710 average time/residue: 1.7645 time to fit residues: 1644.2992 Evaluate side-chains 471 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 465 time to evaluate : 5.120 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 4 average time/residue: 1.3987 time to fit residues: 14.2147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 624 optimal weight: 8.9990 chunk 560 optimal weight: 8.9990 chunk 311 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 378 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 580 optimal weight: 0.7980 chunk 224 optimal weight: 0.5980 chunk 352 optimal weight: 50.0000 chunk 431 optimal weight: 10.0000 chunk 672 optimal weight: 50.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN E 209 HIS F 149 GLN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 GLN H 162 GLN x 91 ASN x 216 GLN ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 269 ASN ** w 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 ASN u 112 HIS u 352 GLN u 575 GLN ** u 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 GLN I 84 ASN I 167 GLN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 10 HIS q 29 ASN q 36 GLN q 167 ASN K 247 HIS K 350 HIS K 527 HIS ** K 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 86022 Z= 0.289 Angle : 0.676 12.661 123632 Z= 0.345 Chirality : 0.041 0.321 15135 Planarity : 0.005 0.113 9840 Dihedral : 21.895 179.716 29698 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 2.07 % Allowed : 10.17 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.05 % Twisted Proline : 0.78 % 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: -0.58 (0.11), residues: 5838 helix: 0.42 (0.10), residues: 2554 sheet: -0.61 (0.18), residues: 810 loop : -1.06 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP w 225 HIS 0.010 0.001 HIS u 617 PHE 0.034 0.002 PHE J 147 TYR 0.026 0.002 TYR K 720 ARG 0.012 0.001 ARG w 418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 510 time to evaluate : 5.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 41 residues processed: 571 average time/residue: 1.7379 time to fit residues: 1324.8037 Evaluate side-chains 511 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 470 time to evaluate : 5.039 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 25 residues processed: 17 average time/residue: 0.8259 time to fit residues: 29.7543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 373 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 559 optimal weight: 4.9990 chunk 457 optimal weight: 20.0000 chunk 185 optimal weight: 3.9990 chunk 673 optimal weight: 30.0000 chunk 727 optimal weight: 40.0000 chunk 599 optimal weight: 20.0000 chunk 667 optimal weight: 50.0000 chunk 229 optimal weight: 0.0170 chunk 540 optimal weight: 0.8980 overall best weight: 1.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN H 162 GLN x 91 ASN x 110 ASN x 217 ASN ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 ASN ** u 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 29 ASN q 167 ASN ** K 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 86022 Z= 0.182 Angle : 0.592 12.235 123632 Z= 0.305 Chirality : 0.037 0.286 15135 Planarity : 0.004 0.111 9840 Dihedral : 21.764 179.918 29698 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 2.30 % Allowed : 12.59 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.05 % Twisted Proline : 0.78 % 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: -0.22 (0.11), residues: 5838 helix: 0.81 (0.10), residues: 2563 sheet: -0.52 (0.18), residues: 799 loop : -0.98 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP w 213 HIS 0.008 0.001 HIS u 617 PHE 0.024 0.001 PHE J 159 TYR 0.033 0.001 TYR f 140 ARG 0.015 0.000 ARG Q 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 508 time to evaluate : 5.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 47 residues processed: 571 average time/residue: 1.6569 time to fit residues: 1277.6173 Evaluate side-chains 509 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 462 time to evaluate : 5.036 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 31 residues processed: 17 average time/residue: 0.8602 time to fit residues: 30.5753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 665 optimal weight: 50.0000 chunk 506 optimal weight: 9.9990 chunk 349 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 321 optimal weight: 4.9990 chunk 452 optimal weight: 10.0000 chunk 675 optimal weight: 9.9990 chunk 715 optimal weight: 10.0000 chunk 352 optimal weight: 30.0000 chunk 640 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 91 ASN X 39 ASN X 46 HIS ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 113 HIS ** u 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 594 ASN ** K1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1127 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 86022 Z= 0.555 Angle : 0.881 12.869 123632 Z= 0.436 Chirality : 0.051 0.516 15135 Planarity : 0.007 0.112 9840 Dihedral : 22.037 178.647 29698 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 3.71 % Allowed : 14.24 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.05 % Twisted Proline : 0.78 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.11), residues: 5838 helix: 0.52 (0.10), residues: 2579 sheet: -0.70 (0.18), residues: 795 loop : -1.22 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP w 213 HIS 0.014 0.002 HIS u 617 PHE 0.085 0.003 PHE J 159 TYR 0.026 0.002 TYR I 198 ARG 0.014 0.001 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 484 time to evaluate : 5.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 190 outliers final: 86 residues processed: 607 average time/residue: 1.6424 time to fit residues: 1352.1766 Evaluate side-chains 548 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 462 time to evaluate : 5.146 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 62 residues processed: 25 average time/residue: 1.0514 time to fit residues: 46.6314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 595 optimal weight: 6.9990 chunk 406 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 532 optimal weight: 0.0570 chunk 295 optimal weight: 0.9980 chunk 610 optimal weight: 6.9990 chunk 494 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 365 optimal weight: 50.0000 chunk 642 optimal weight: 30.0000 chunk 180 optimal weight: 7.9990 overall best weight: 2.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 91 ASN ** w 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 529 GLN ** u 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 86022 Z= 0.242 Angle : 0.643 12.756 123632 Z= 0.328 Chirality : 0.039 0.313 15135 Planarity : 0.005 0.111 9840 Dihedral : 21.817 177.946 29698 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 3.18 % Allowed : 16.18 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.05 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 5838 helix: 0.82 (0.10), residues: 2571 sheet: -0.69 (0.18), residues: 796 loop : -1.03 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP w 213 HIS 0.009 0.001 HIS w 321 PHE 0.038 0.002 PHE K 888 TYR 0.022 0.001 TYR Q 95 ARG 0.010 0.000 ARG q 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 486 time to evaluate : 5.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 88 residues processed: 597 average time/residue: 1.6069 time to fit residues: 1301.2610 Evaluate side-chains 552 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 464 time to evaluate : 5.143 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 70 residues processed: 21 average time/residue: 0.8881 time to fit residues: 36.8536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 240 optimal weight: 6.9990 chunk 644 optimal weight: 40.0000 chunk 141 optimal weight: 10.0000 chunk 419 optimal weight: 0.1980 chunk 176 optimal weight: 10.0000 chunk 715 optimal weight: 6.9990 chunk 594 optimal weight: 10.0000 chunk 331 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 236 optimal weight: 0.9980 chunk 375 optimal weight: 2.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS E 138 HIS F 149 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN x 91 ASN ** w 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 ASN ** u 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 352 GLN ** u 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 86022 Z= 0.298 Angle : 0.674 12.445 123632 Z= 0.343 Chirality : 0.041 0.331 15135 Planarity : 0.005 0.111 9840 Dihedral : 21.785 178.560 29698 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 3.08 % Allowed : 17.21 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.05 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 5838 helix: 0.88 (0.10), residues: 2574 sheet: -0.70 (0.18), residues: 805 loop : -1.00 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP w 225 HIS 0.011 0.001 HIS w 321 PHE 0.035 0.002 PHE H 135 TYR 0.025 0.002 TYR f 140 ARG 0.011 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 475 time to evaluate : 5.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 158 outliers final: 92 residues processed: 593 average time/residue: 1.6237 time to fit residues: 1306.2989 Evaluate side-chains 552 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 460 time to evaluate : 5.079 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 77 residues processed: 17 average time/residue: 0.8521 time to fit residues: 30.3400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 690 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 407 optimal weight: 9.9990 chunk 522 optimal weight: 0.9980 chunk 405 optimal weight: 6.9990 chunk 602 optimal weight: 10.0000 chunk 399 optimal weight: 1.9990 chunk 713 optimal weight: 0.9980 chunk 446 optimal weight: 30.0000 chunk 434 optimal weight: 5.9990 chunk 329 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 62 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN ** Z 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 91 ASN ** w 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 ASN ** u 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN q 262 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 86022 Z= 0.231 Angle : 0.631 12.336 123632 Z= 0.322 Chirality : 0.039 0.308 15135 Planarity : 0.005 0.111 9840 Dihedral : 21.718 178.861 29698 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 2.75 % Allowed : 18.05 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.05 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.11), residues: 5838 helix: 0.98 (0.11), residues: 2575 sheet: -0.70 (0.18), residues: 806 loop : -0.94 (0.12), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP w 225 HIS 0.007 0.001 HIS u 617 PHE 0.034 0.001 PHE H 135 TYR 0.029 0.001 TYR f 140 ARG 0.013 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 482 time to evaluate : 5.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 89 residues processed: 587 average time/residue: 1.6102 time to fit residues: 1288.6375 Evaluate side-chains 547 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 458 time to evaluate : 5.121 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 78 residues processed: 14 average time/residue: 0.8731 time to fit residues: 26.5374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 441 optimal weight: 8.9990 chunk 284 optimal weight: 3.9990 chunk 425 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 453 optimal weight: 3.9990 chunk 485 optimal weight: 5.9990 chunk 352 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 560 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN ** Z 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 91 ASN ** w 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 ASN u 112 HIS ** u 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 86022 Z= 0.297 Angle : 0.680 13.098 123632 Z= 0.344 Chirality : 0.041 0.326 15135 Planarity : 0.005 0.111 9840 Dihedral : 21.718 178.318 29698 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 2.69 % Allowed : 18.69 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.05 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 5838 helix: 0.94 (0.10), residues: 2576 sheet: -0.72 (0.18), residues: 805 loop : -0.98 (0.12), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP w 225 HIS 0.008 0.001 HIS u 617 PHE 0.034 0.002 PHE H 135 TYR 0.031 0.002 TYR S 95 ARG 0.014 0.001 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 461 time to evaluate : 5.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 98 residues processed: 570 average time/residue: 1.5961 time to fit residues: 1245.2476 Evaluate side-chains 541 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 443 time to evaluate : 5.066 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 86 residues processed: 16 average time/residue: 0.9449 time to fit residues: 30.5548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 648 optimal weight: 10.0000 chunk 683 optimal weight: 30.0000 chunk 623 optimal weight: 8.9990 chunk 664 optimal weight: 40.0000 chunk 400 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 chunk 521 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 600 optimal weight: 0.2980 chunk 628 optimal weight: 10.0000 chunk 662 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN ** Z 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 ASN u 112 HIS u 352 GLN ** u 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 86022 Z= 0.237 Angle : 0.644 13.158 123632 Z= 0.326 Chirality : 0.039 0.308 15135 Planarity : 0.005 0.111 9840 Dihedral : 21.660 178.949 29698 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 2.38 % Allowed : 19.34 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.05 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 5838 helix: 1.00 (0.11), residues: 2577 sheet: -0.71 (0.18), residues: 806 loop : -0.93 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP w 225 HIS 0.006 0.001 HIS u 144 PHE 0.031 0.001 PHE H 135 TYR 0.036 0.001 TYR f 140 ARG 0.014 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 463 time to evaluate : 5.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 89 residues processed: 558 average time/residue: 1.6132 time to fit residues: 1230.3546 Evaluate side-chains 534 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 445 time to evaluate : 5.315 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 78 residues processed: 14 average time/residue: 0.8799 time to fit residues: 26.9219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 436 optimal weight: 5.9990 chunk 702 optimal weight: 10.0000 chunk 428 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 488 optimal weight: 9.9990 chunk 737 optimal weight: 7.9990 chunk 678 optimal weight: 30.0000 chunk 587 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 453 optimal weight: 8.9990 chunk 359 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN G 163 ASN ** Z 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 ASN u 112 HIS u 352 GLN ** u 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** Q 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN I 167 GLN ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 86022 Z= 0.441 Angle : 0.797 18.794 123632 Z= 0.396 Chirality : 0.046 0.371 15135 Planarity : 0.006 0.112 9840 Dihedral : 21.804 179.163 29698 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 2.13 % Allowed : 19.67 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.05 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.11), residues: 5838 helix: 0.84 (0.10), residues: 2576 sheet: -0.73 (0.18), residues: 803 loop : -1.08 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP w 225 HIS 0.012 0.001 HIS u 617 PHE 0.041 0.002 PHE H 135 TYR 0.042 0.002 TYR S 95 ARG 0.014 0.001 ARG c 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11676 Ramachandran restraints generated. 5838 Oldfield, 0 Emsley, 5838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 451 time to evaluate : 5.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 82 residues processed: 543 average time/residue: 1.6600 time to fit residues: 1224.9843 Evaluate side-chains 517 residues out of total 5161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 435 time to evaluate : 5.060 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 79 residues processed: 6 average time/residue: 0.8691 time to fit residues: 15.0198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 466 optimal weight: 0.8980 chunk 625 optimal weight: 0.7980 chunk 179 optimal weight: 8.9990 chunk 541 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 587 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 603 optimal weight: 30.0000 chunk 74 optimal weight: 8.9990 chunk 108 optimal weight: 50.0000 overall best weight: 4.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN ** Z 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 112 HIS u 352 GLN ** u 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** Q 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** q 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.171137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.157104 restraints weight = 122384.987| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 0.65 r_work: 0.4066 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 86022 Z= 0.328 Angle : 0.718 16.789 123632 Z= 0.360 Chirality : 0.042 0.336 15135 Planarity : 0.005 0.111 9840 Dihedral : 21.750 178.750 29698 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 2.11 % Allowed : 19.80 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.05 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 5838 helix: 0.88 (0.11), residues: 2576 sheet: -0.72 (0.18), residues: 802 loop : -1.05 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP w 225 HIS 0.008 0.001 HIS u 617 PHE 0.039 0.002 PHE H 135 TYR 0.042 0.002 TYR S 95 ARG 0.021 0.001 ARG H 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20643.44 seconds wall clock time: 363 minutes 2.66 seconds (21782.66 seconds total)