Starting phenix.real_space_refine on Thu Dec 14 14:03:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/12_2023/7wtt_32800_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/12_2023/7wtt_32800.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/12_2023/7wtt_32800_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/12_2023/7wtt_32800_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/12_2023/7wtt_32800_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/12_2023/7wtt_32800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/12_2023/7wtt_32800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/12_2023/7wtt_32800_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/12_2023/7wtt_32800_updated.pdb" } resolution = 3.1 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 234 5.16 5 C 46811 2.51 5 N 15279 2.21 5 O 19777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 75": "OE1" <-> "OE2" Residue "E TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "q TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 83677 Number of models: 1 Model: "" Number of chains: 36 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: "a" Number of atoms: 2462 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 297, 2456 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 9, 'TRANS': 287} Conformer: "B" Number of residues, atoms: 297, 2456 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 9, 'TRANS': 287} bond proxies already assigned to first conformer: 2507 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 121 192.024 134.390 29.492 1.00 17.51 S ATOM 80333 SG CYS f 126 191.184 133.159 33.203 1.00 19.87 S ATOM 80451 SG CYS f 141 188.773 134.418 30.751 1.00 19.89 S ATOM 80470 SG CYS f 144 191.049 136.911 32.379 1.00 18.39 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER a 122 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER a 122 " occ=0.50 residue: pdb=" N GLY a 183 " occ=0.97 ... (2 atoms not shown) pdb=" O GLY a 183 " occ=0.97 residue: pdb=" N THR a 184 " occ=0.87 ... (5 atoms not shown) pdb=" CG2 THR a 184 " occ=0.87 Time building chain proxies: 33.28, per 1000 atoms: 0.40 Number of scatterers: 83677 At special positions: 0 Unit cell: (255.219, 254.16, 204.387, 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 234 16.00 P 1575 15.00 O 19777 8.00 N 15279 7.00 C 46811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.34 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 141 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 144 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 126 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 121 " Number of angles added : 6 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 250 helices and 50 sheets defined 41.3% alpha, 12.2% beta 504 base pairs and 888 stacking pairs defined. Time for finding SS restraints: 32.73 Creating SS restraints... Processing helix chain 'R' and resid 7 through 20 Processing helix chain 'R' and resid 28 through 38 Processing helix chain 'R' and resid 44 through 61 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 61 No H-bonds generated for 'chain 'B' and resid 58 through 61' Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' 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 225 through 232 Processing helix chain 'E' and resid 11 through 13 No H-bonds generated for 'chain 'E' and resid 11 through 13' 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 50 Processing helix chain 'E' and resid 58 through 66 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 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' 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 33 through 35 No H-bonds generated for 'chain 'F' and resid 33 through 35' Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 87 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 181 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'H' and resid 18 through 33 Processing helix chain 'H' and resid 69 through 74 removed outlier: 3.536A pdb=" N LYS H 74 " --> pdb=" O LYS H 70 " (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 133 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 170 through 181 Processing helix chain 'G' and resid 21 through 23 No H-bonds generated for 'chain 'G' and resid 21 through 23' Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' 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 79 through 85 Processing helix chain 'Y' and resid 88 through 93 Processing helix chain 'Y' and resid 104 through 116 removed outlier: 4.048A 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 92 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 165 through 167 No H-bonds generated for 'chain 'x' and resid 165 through 167' Processing helix chain 'x' and resid 174 through 184 Processing helix chain 'x' and resid 186 through 198 removed outlier: 6.336A pdb=" N THR x 190 " --> pdb=" O GLY x 187 " (cutoff:3.500A) Processing helix chain 'x' and resid 215 through 228 Processing helix chain 'x' and resid 234 through 244 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 removed outlier: 3.521A pdb=" N ALA X 38 " --> pdb=" O THR X 34 " (cutoff:3.500A) No H-bonds generated for '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 26 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: 4.185A 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 222 through 224 No H-bonds generated for 'chain 'w' and resid 222 through 224' 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 297 Processing helix chain 'w' and resid 302 through 314 Processing helix chain 'w' and resid 319 through 330 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 390 through 392 No H-bonds generated for 'chain 'w' and resid 390 through 392' 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 43 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 211 removed outlier: 4.327A pdb=" N ILE u 201 " --> pdb=" O LEU u 197 " (cutoff:3.500A) removed outlier: 5.505A 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 404 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 545 Processing helix chain 'u' and resid 567 through 575 removed outlier: 3.528A pdb=" N GLN u 575 " --> pdb=" O GLU u 571 " (cutoff:3.500A) Processing helix chain 'u' and resid 720 through 725 removed outlier: 3.832A pdb=" N LEU u 724 " --> pdb=" O ARG u 720 " (cutoff:3.500A) Processing helix chain 't' and resid 292 through 301 Processing helix chain 't' and resid 353 through 355 No H-bonds generated for 'chain 't' and resid 353 through 355' 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 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 48 Processing helix chain 'S' and resid 56 through 58 No H-bonds generated for 'chain 'S' and resid 56 through 58' Processing helix chain 'S' and resid 61 through 72 Processing helix chain 'S' and resid 74 through 77 Processing helix chain 'S' and resid 102 through 116 Processing helix chain 'S' and resid 120 through 127 Processing helix chain 'Q' and resid 39 through 41 No H-bonds generated for 'chain 'Q' and resid 39 through 41' Processing helix chain 'Q' and resid 48 through 58 Proline residue: Q 54 - end of helix 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 27 Processing helix chain 'P' and resid 34 through 36 No H-bonds generated for 'chain 'P' and resid 34 through 36' Processing helix chain 'P' and resid 39 through 46 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 116 through 119 Processing helix chain 'O' and resid 65 through 67 No H-bonds generated for 'chain 'O' and resid 65 through 67' 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 66 No H-bonds generated for 'chain 'N' and resid 63 through 66' Processing helix chain 'N' and resid 71 through 78 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 61 Processing helix chain 'J' and resid 68 through 83 Processing helix chain 'J' and resid 94 through 99 removed outlier: 3.796A pdb=" N LEU J 98 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 3.766A 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 154 through 156 No H-bonds generated for 'chain 'J' and resid 154 through 156' Processing helix chain 'J' and resid 172 through 178 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 154 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 88 Processing helix 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 27 Processing helix chain 'q' and resid 30 through 46 Processing helix chain 'q' and resid 66 through 73 Processing helix chain 'q' and resid 85 through 93 Processing helix chain 'q' and resid 125 through 128 Processing helix chain 'q' and resid 138 through 152 Processing helix chain 'q' and resid 168 through 181 Processing helix chain 'q' and resid 250 through 261 Processing helix chain 'K' and resid 109 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 138 through 140 No H-bonds generated for 'chain 'K' and resid 138 through 140' Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 152 through 155 No H-bonds generated for 'chain 'K' and resid 152 through 155' Processing helix chain 'K' and resid 164 through 176 removed outlier: 4.287A pdb=" N LYS K 176 " --> pdb=" O ASN K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'K' and resid 187 through 204 Processing helix chain 'K' and resid 208 through 223 Processing helix chain 'K' and resid 233 through 244 removed outlier: 4.211A 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 302 through 314 removed outlier: 3.851A pdb=" N HIS K 306 " --> pdb=" O THR K 302 " (cutoff:3.500A) 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: 3.595A pdb=" N TYR K 375 " --> pdb=" O ILE K 371 " (cutoff:3.500A) removed outlier: 4.816A 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: 3.997A 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 448 through 454 removed outlier: 4.581A pdb=" N ALA K 452 " --> pdb=" O PRO K 449 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 479 removed outlier: 3.989A pdb=" N LEU K 479 " --> pdb=" O VAL K 475 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 521 removed outlier: 6.265A pdb=" N ARG K 503 " --> pdb=" O GLU K 499 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN K 504 " --> pdb=" O ALA K 500 " (cutoff:3.500A) Proline residue: K 507 - end of helix removed outlier: 3.990A pdb=" N ARG K 510 " --> pdb=" O HIS K 506 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS K 511 " --> pdb=" O PRO K 507 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N CYS K 512 " --> pdb=" O VAL K 508 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG K 520 " --> pdb=" O LEU K 516 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU K 521 " --> pdb=" O CYS K 517 " (cutoff:3.500A) Processing helix chain 'K' and resid 528 through 541 Processing helix chain 'K' and resid 544 through 550 Processing helix chain 'K' and resid 567 through 576 removed outlier: 3.657A pdb=" N LEU K 570 " --> pdb=" O SER K 567 " (cutoff:3.500A) Proline residue: K 571 - end of helix Processing helix chain 'K' and resid 582 through 605 Proline residue: K 591 - end of helix Processing helix chain 'K' and resid 609 through 623 removed outlier: 3.753A pdb=" N LYS K 613 " --> pdb=" O THR K 609 " (cutoff:3.500A) Processing helix chain 'K' and resid 625 through 629 Processing helix chain 'K' and resid 636 through 639 No H-bonds generated for 'chain 'K' and resid 636 through 639' Processing helix chain 'K' and resid 644 through 652 Processing helix chain 'K' and resid 655 through 671 removed outlier: 5.608A pdb=" N VAL K 659 " --> pdb=" O ASP K 656 " (cutoff:3.500A) Processing helix chain 'K' and resid 676 through 697 removed outlier: 4.679A 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 763 Proline residue: K 762 - end of helix Processing helix chain 'K' and resid 766 through 781 Proline residue: K 778 - end of helix removed outlier: 4.919A 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 844 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: 3.668A 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 978 No H-bonds generated for 'chain 'K' and resid 975 through 978' Processing helix chain 'K' and resid 982 through 990 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: 3.970A pdb=" N ARG K1030 " --> pdb=" O GLU K1026 " (cutoff:3.500A) removed outlier: 3.962A 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 16 through 28 removed outlier: 4.056A pdb=" N GLU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 43 Processing helix chain 'M' and resid 59 through 62 No H-bonds generated for 'chain 'M' and resid 59 through 62' 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 'a' and resid 57 through 66 Processing helix chain 'a' and resid 97 through 103 Processing helix chain 'a' and resid 110 through 129 Processing helix chain 'a' and resid 147 through 151 removed outlier: 3.535A pdb=" N CYS a 150 " --> pdb=" O GLY a 147 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN a 151 " --> pdb=" O ARG a 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 147 through 151' Processing helix chain 'a' and resid 158 through 160 No H-bonds generated for 'chain 'a' and resid 158 through 160' Processing helix chain 'a' and resid 190 through 194 Processing helix chain 'a' and resid 200 through 216 Processing helix chain 'a' and resid 229 through 241 Processing helix chain 'a' and resid 246 through 249 Processing helix chain 'a' and resid 254 through 264 Processing helix chain 'a' and resid 274 through 287 Processing helix chain 'a' and resid 297 through 304 Processing helix chain 'z' and resid 104 through 128 Processing helix chain 'z' and resid 178 through 180 No H-bonds generated for 'chain 'z' and resid 178 through 180' 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: 4.852A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.152A 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: 6.630A pdb=" N VAL B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL B 212 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 29 through 34 Processing sheet with id= E, first strand: chain 'c' and resid 55 through 58 removed outlier: 6.657A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 7.171A 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 89 through 92 Processing sheet with id= H, first strand: chain 'E' and resid 121 through 125 removed outlier: 6.173A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.340A 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: 7.229A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN E 179 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.330A 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 92 through 96 removed outlier: 8.905A pdb=" N VAL H 93 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) 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: 7.114A 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: 7.046A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Y' and resid 5 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: 6.432A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA X 103 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 5.389A 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 removed outlier: 4.036A pdb=" N GLU W 49 " --> pdb=" O ASN W 64 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.457A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 5.874A 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: 9.499A pdb=" N LEU u 221 " --> pdb=" O TYR u 185 " (cutoff:3.500A) removed outlier: 6.670A 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: 3.720A pdb=" N SER u 263 " --> pdb=" O VAL u 269 " (cutoff:3.500A) removed outlier: 7.906A 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: 6.175A pdb=" N VAL u 597 " --> pdb=" O LEU u 684 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU u 684 " --> pdb=" O VAL u 597 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU u 667 " --> pdb=" O ILE u 679 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR u 681 " --> pdb=" O VAL u 665 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL u 665 " --> pdb=" O THR u 681 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLN u 670 " --> pdb=" O GLU u 613 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N GLU u 613 " --> pdb=" O GLN u 670 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'u' and resid 693 through 701 Processing sheet with id= AE, first strand: chain 'u' and resid 702 through 707 removed outlier: 6.647A pdb=" N VAL u 712 " --> pdb=" O PHE u 704 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE u 706 " --> pdb=" O MET u 710 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N MET u 710 " --> pdb=" O ILE u 706 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N SER u 754 " --> pdb=" O ILE u 741 " (cutoff:3.500A) removed outlier: 5.624A 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 116 removed outlier: 5.348A pdb=" N GLY T 120 " --> pdb=" O ASP T 116 " (cutoff:3.500A) 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 76 through 78 Processing sheet with id= AK, first strand: chain 'O' and resid 52 through 56 removed outlier: 6.635A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA O 92 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N CYS O 31 " --> pdb=" O ALA O 92 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS O 94 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE O 33 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS O 96 " --> pdb=" O ILE O 33 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ALA O 35 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 6.904A 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: 17.912A pdb=" N ILE L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.343A pdb=" N LEU L 93 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N SER L 74 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP L 91 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL L 87 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG L 139 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N HIS L 112 " --> pdb=" O ARG L 139 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN L 141 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'J' and resid 135 through 137 Processing sheet with id= AN, first strand: chain 'I' and resid 62 through 66 Processing sheet with id= AO, first strand: chain 'I' and resid 187 through 189 removed outlier: 6.180A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 42 through 48 removed outlier: 6.368A pdb=" N HIS I 44 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA I 57 " --> pdb=" O HIS I 44 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL I 46 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR I 55 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL I 48 " --> pdb=" O LYS I 53 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS I 53 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'r' and resid 30 through 32 Processing sheet with id= AR, first strand: chain 'r' and resid 106 through 110 removed outlier: 4.043A pdb=" N GLU r 95 " --> pdb=" O GLU r 29 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU r 29 " --> pdb=" O GLU r 95 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR r 97 " --> pdb=" O ALA r 27 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA r 27 " --> pdb=" O THR r 97 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN r 99 " --> pdb=" O LEU r 25 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU r 25 " --> pdb=" O GLN r 99 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'q' and resid 184 through 190 removed outlier: 6.637A pdb=" N TYR q 77 " --> pdb=" O LEU q 57 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASP q 59 " --> pdb=" O TYR q 77 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL q 79 " --> pdb=" O ASP q 59 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP q 99 " --> pdb=" O GLY q 80 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ASP q 82 " --> pdb=" O ASP q 99 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU q 101 " --> pdb=" O ASP q 82 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'M' and resid 31 through 33 removed outlier: 6.542A pdb=" N ASN M 75 " --> pdb=" O CYS M 50 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU M 52 " --> pdb=" O ASN M 75 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE M 77 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'f' and resid 132 through 135 Processing sheet with id= AV, first strand: chain 'a' and resid 17 through 19 removed outlier: 6.528A pdb=" N ASP a 91 " --> pdb=" O ILE a 76 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE a 76 " --> pdb=" O ASP a 91 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'a' and resid 142 through 144 Processing sheet with id= AX, first strand: chain 'a' and resid 22 through 26 removed outlier: 6.993A pdb=" N ILE a 31 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N SER a 25 " --> pdb=" O GLY a 29 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY a 29 " --> pdb=" O SER a 25 " (cutoff:3.500A) 2023 hydrogen bonds defined for protein. 5731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1245 hydrogen bonds 1926 hydrogen bond angles 0 basepair planarities 504 basepair parallelities 888 stacking parallelities Total time for adding SS restraints: 62.69 Time building geometry restraints manager: 34.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 10510 1.31 - 1.44: 32281 1.44 - 1.57: 42255 1.57 - 1.70: 3132 1.70 - 1.83: 365 Bond restraints: 88543 Sorted by residual: bond pdb=" C4' G7M 21639 " pdb=" C3' G7M 21639 " ideal model delta sigma weight residual 1.527 1.258 0.269 1.50e-02 4.44e+03 3.21e+02 bond pdb=" C2' G7M 21639 " pdb=" C1' G7M 21639 " ideal model delta sigma weight residual 1.526 1.282 0.244 1.50e-02 4.44e+03 2.65e+02 bond pdb=" C3' G7M 21639 " pdb=" C2' G7M 21639 " ideal model delta sigma weight residual 1.525 1.664 -0.139 1.50e-02 4.44e+03 8.60e+01 bond pdb=" O4' G7M 21639 " pdb=" C1' G7M 21639 " ideal model delta sigma weight residual 1.415 1.543 -0.128 1.50e-02 4.44e+03 7.28e+01 bond pdb=" C4' G7M 21639 " pdb=" O4' G7M 21639 " ideal model delta sigma weight residual 1.454 1.565 -0.111 1.50e-02 4.44e+03 5.47e+01 ... (remaining 88538 not shown) Histogram of bond angle deviations from ideal: 94.57 - 102.82: 3017 102.82 - 111.08: 41402 111.08 - 119.33: 40435 119.33 - 127.58: 38823 127.58 - 135.84: 3343 Bond angle restraints: 127020 Sorted by residual: angle pdb=" O PRO q 13 " pdb=" C PRO q 13 " pdb=" N PRO q 14 " ideal model delta sigma weight residual 121.15 117.68 3.47 4.70e-01 4.53e+00 5.46e+01 angle pdb=" CA GLN H 162 " pdb=" CB GLN H 162 " pdb=" CG GLN H 162 " ideal model delta sigma weight residual 114.10 126.70 -12.60 2.00e+00 2.50e-01 3.97e+01 angle pdb=" CA PRO Z 63 " pdb=" N PRO Z 63 " pdb=" CD PRO Z 63 " ideal model delta sigma weight residual 112.00 103.27 8.73 1.40e+00 5.10e-01 3.89e+01 angle pdb=" O3' U 21494 " pdb=" C3' U 21494 " pdb=" C2' U 21494 " ideal model delta sigma weight residual 109.50 118.24 -8.74 1.50e+00 4.44e-01 3.39e+01 angle pdb=" N PRO Z 63 " pdb=" CD PRO Z 63 " pdb=" CG PRO Z 63 " ideal model delta sigma weight residual 103.20 94.57 8.63 1.50e+00 4.44e-01 3.31e+01 ... (remaining 127015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 50494 35.83 - 71.67: 3582 71.67 - 107.50: 495 107.50 - 143.33: 19 143.33 - 179.16: 24 Dihedral angle restraints: 54614 sinusoidal: 36513 harmonic: 18101 Sorted by residual: 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 200.00 21.47 178.53 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual 200.00 30.41 169.59 1 1.50e+01 4.44e-03 8.46e+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 6.34 -166.34 1 1.50e+01 4.44e-03 8.41e+01 ... (remaining 54611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 14243 0.089 - 0.178: 1134 0.178 - 0.268: 80 0.268 - 0.357: 27 0.357 - 0.446: 2 Chirality restraints: 15486 Sorted by residual: chirality pdb=" CB ILE u 274 " pdb=" CA ILE u 274 " pdb=" CG1 ILE u 274 " pdb=" CG2 ILE u 274 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.97e+00 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 -2.37 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C3' A 2 604 " pdb=" C4' A 2 604 " pdb=" O3' A 2 604 " pdb=" C2' A 2 604 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 15483 not shown) Planarity restraints: 10272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' G7M 21639 " 1.018 2.00e-02 2.50e+03 6.58e-01 9.75e+03 pdb=" C4' G7M 21639 " -0.162 2.00e-02 2.50e+03 pdb=" O4' G7M 21639 " -1.018 2.00e-02 2.50e+03 pdb=" C3' G7M 21639 " 0.238 2.00e-02 2.50e+03 pdb=" O3' G7M 21639 " -0.829 2.00e-02 2.50e+03 pdb=" C2' G7M 21639 " 0.573 2.00e-02 2.50e+03 pdb=" O2' G7M 21639 " 0.722 2.00e-02 2.50e+03 pdb=" C1' G7M 21639 " -0.445 2.00e-02 2.50e+03 pdb=" N9 G7M 21639 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 102 " 0.051 2.00e-02 2.50e+03 2.35e-02 1.51e+01 pdb=" N9 A 2 102 " -0.054 2.00e-02 2.50e+03 pdb=" C8 A 2 102 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A 2 102 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A 2 102 " -0.009 2.00e-02 2.50e+03 pdb=" C6 A 2 102 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A 2 102 " 0.018 2.00e-02 2.50e+03 pdb=" N1 A 2 102 " 0.008 2.00e-02 2.50e+03 pdb=" C2 A 2 102 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A 2 102 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A 2 102 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 45 " -0.053 2.00e-02 2.50e+03 2.31e-02 1.47e+01 pdb=" N9 A 2 45 " 0.050 2.00e-02 2.50e+03 pdb=" C8 A 2 45 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A 2 45 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A 2 45 " 0.006 2.00e-02 2.50e+03 pdb=" C6 A 2 45 " -0.010 2.00e-02 2.50e+03 pdb=" N6 A 2 45 " -0.014 2.00e-02 2.50e+03 pdb=" N1 A 2 45 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A 2 45 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 2 45 " 0.009 2.00e-02 2.50e+03 pdb=" C4 A 2 45 " 0.011 2.00e-02 2.50e+03 ... (remaining 10269 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 1601 2.63 - 3.20: 66825 3.20 - 3.77: 152260 3.77 - 4.33: 204862 4.33 - 4.90: 294945 Nonbonded interactions: 720493 Sorted by model distance: nonbonded pdb=" O4 U 2 749 " pdb=" O6 G 2 793 " model vdw 2.066 3.040 nonbonded pdb=" O2 U 2 885 " pdb=" O6 G 2 901 " model vdw 2.189 2.432 nonbonded pdb=" O2' G 2 798 " pdb=" OG SER H 108 " model vdw 2.200 2.440 nonbonded pdb=" O2' U 2 160 " pdb=" OP2 C 2 162 " model vdw 2.201 2.440 nonbonded pdb=" O2' C 21811 " pdb=" OE1 GLN u 63 " model vdw 2.203 2.440 ... (remaining 720488 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=0.47 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: 2.760 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: 12.660 Check model and map are aligned: 0.930 Set scattering table: 0.610 Process input model: 235.980 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.220 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: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 258.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 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 0.269 88543 Z= 0.381 Angle : 0.922 14.283 127020 Z= 0.483 Chirality : 0.051 0.446 15486 Planarity : 0.010 0.658 10272 Dihedral : 20.817 179.163 42886 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.99 % Favored : 95.96 % Rotamer: Outliers : 0.46 % Allowed : 0.80 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.05 % Twisted Proline : 0.37 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.10), residues: 6136 helix: -0.47 (0.09), residues: 2686 sheet: -0.47 (0.17), residues: 819 loop : -1.29 (0.11), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP w 286 HIS 0.020 0.002 HIS r 6 PHE 0.034 0.003 PHE K 194 TYR 0.058 0.002 TYR B 205 ARG 0.015 0.001 ARG L 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 669 time to evaluate : 5.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 2 residues processed: 681 average time/residue: 0.8109 time to fit residues: 931.3206 Evaluate side-chains 538 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 536 time to evaluate : 5.329 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5885 time to fit residues: 8.9293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 649 optimal weight: 10.0000 chunk 582 optimal weight: 50.0000 chunk 323 optimal weight: 0.9990 chunk 199 optimal weight: 20.0000 chunk 393 optimal weight: 0.9980 chunk 311 optimal weight: 7.9990 chunk 602 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 chunk 366 optimal weight: 30.0000 chunk 448 optimal weight: 7.9990 chunk 698 optimal weight: 50.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN F 137 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 ASN u 226 GLN u 256 HIS u 290 HIS u 301 GLN ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN S 76 GLN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 527 HIS f 135 HIS ** a 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 261 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 88543 Z= 0.401 Angle : 0.759 15.712 127020 Z= 0.383 Chirality : 0.045 0.354 15486 Planarity : 0.006 0.134 10272 Dihedral : 21.933 179.969 30036 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.04 % Rotamer: Outliers : 1.26 % Allowed : 8.76 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.05 % Twisted Proline : 0.37 % 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: -0.79 (0.10), residues: 6136 helix: 0.21 (0.10), residues: 2687 sheet: -0.44 (0.18), residues: 800 loop : -1.26 (0.11), residues: 2649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP u 133 HIS 0.015 0.002 HIS P 79 PHE 0.039 0.002 PHE J 147 TYR 0.032 0.002 TYR B 205 ARG 0.019 0.001 ARG O 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 549 time to evaluate : 5.341 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: 68 outliers final: 54 residues processed: 581 average time/residue: 0.8562 time to fit residues: 846.6825 Evaluate side-chains 579 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 525 time to evaluate : 5.319 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.6139 time to fit residues: 70.4075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 388 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 581 optimal weight: 30.0000 chunk 475 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 699 optimal weight: 8.9990 chunk 755 optimal weight: 8.9990 chunk 623 optimal weight: 20.0000 chunk 693 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 chunk 561 optimal weight: 0.5980 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 46 HIS u 226 GLN ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN T 137 GLN S 11 HIS ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 ASN J 27 GLN r 99 GLN q 132 ASN K 527 HIS ** a 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 88543 Z= 0.391 Angle : 0.741 15.532 127020 Z= 0.374 Chirality : 0.045 0.353 15486 Planarity : 0.006 0.138 10272 Dihedral : 21.918 179.454 30036 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.32 % Favored : 95.66 % Rotamer: Outliers : 1.47 % Allowed : 12.01 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.05 % Twisted Proline : 0.37 % 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: -0.59 (0.10), residues: 6136 helix: 0.50 (0.10), residues: 2682 sheet: -0.40 (0.18), residues: 786 loop : -1.26 (0.11), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP u 133 HIS 0.018 0.002 HIS P 79 PHE 0.038 0.002 PHE J 147 TYR 0.023 0.002 TYR I 198 ARG 0.013 0.001 ARG O 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 568 time to evaluate : 5.493 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: 79 outliers final: 44 residues processed: 624 average time/residue: 0.8161 time to fit residues: 867.4326 Evaluate side-chains 588 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 544 time to evaluate : 5.859 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.6446 time to fit residues: 59.9978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 691 optimal weight: 20.0000 chunk 525 optimal weight: 1.9990 chunk 363 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 chunk 333 optimal weight: 1.9990 chunk 469 optimal weight: 8.9990 chunk 702 optimal weight: 6.9990 chunk 743 optimal weight: 30.0000 chunk 366 optimal weight: 50.0000 chunk 665 optimal weight: 30.0000 chunk 200 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 131 HIS ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 GLN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 99 GLN K 338 HIS K 527 HIS K1127 GLN ** a 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 88543 Z= 0.371 Angle : 0.722 15.711 127020 Z= 0.365 Chirality : 0.044 0.350 15486 Planarity : 0.006 0.136 10272 Dihedral : 21.895 179.896 30036 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.32 % Favored : 95.66 % Rotamer: Outliers : 1.52 % Allowed : 13.72 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.05 % Twisted Proline : 0.37 % 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: -0.46 (0.10), residues: 6136 helix: 0.65 (0.10), residues: 2674 sheet: -0.41 (0.18), residues: 798 loop : -1.22 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP w 213 HIS 0.014 0.001 HIS P 79 PHE 0.035 0.002 PHE J 147 TYR 0.023 0.002 TYR I 198 ARG 0.012 0.001 ARG O 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 552 time to evaluate : 5.384 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: 82 outliers final: 54 residues processed: 610 average time/residue: 0.8123 time to fit residues: 847.7356 Evaluate side-chains 583 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 529 time to evaluate : 5.271 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.6483 time to fit residues: 74.2479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 619 optimal weight: 20.0000 chunk 421 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 553 optimal weight: 0.9980 chunk 306 optimal weight: 10.0000 chunk 634 optimal weight: 50.0000 chunk 513 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 379 optimal weight: 1.9990 chunk 667 optimal weight: 40.0000 chunk 187 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 ASN H 68 GLN x 110 ASN w 27 ASN w 212 ASN ** u 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 527 HIS ** a 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 88543 Z= 0.208 Angle : 0.614 14.733 127020 Z= 0.315 Chirality : 0.038 0.311 15486 Planarity : 0.005 0.112 10272 Dihedral : 21.790 179.783 30036 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 1.02 % Allowed : 14.68 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.05 % Twisted Proline : 0.37 % 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: -0.20 (0.11), residues: 6136 helix: 0.89 (0.10), residues: 2668 sheet: -0.36 (0.18), residues: 802 loop : -1.07 (0.12), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP w 213 HIS 0.012 0.001 HIS P 79 PHE 0.023 0.001 PHE J 147 TYR 0.019 0.001 TYR R 53 ARG 0.007 0.000 ARG I 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 571 time to evaluate : 5.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 24 residues processed: 608 average time/residue: 0.8455 time to fit residues: 874.0467 Evaluate side-chains 566 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 542 time to evaluate : 5.973 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.6231 time to fit residues: 35.9502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 250 optimal weight: 7.9990 chunk 669 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 436 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 744 optimal weight: 10.0000 chunk 617 optimal weight: 0.8980 chunk 344 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 246 optimal weight: 9.9990 chunk 390 optimal weight: 8.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 110 ASN w 27 ASN W 15 ASN u 190 GLN ** u 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 ASN N 90 HIS J 27 GLN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 527 HIS ** a 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 88543 Z= 0.411 Angle : 0.755 15.562 127020 Z= 0.378 Chirality : 0.045 0.364 15486 Planarity : 0.006 0.155 10272 Dihedral : 21.855 179.347 30036 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.70 % Favored : 95.29 % Rotamer: Outliers : 1.47 % Allowed : 15.87 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.05 % Twisted Proline : 0.37 % Twisted General : 0.03 % 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: 6136 helix: 0.80 (0.10), residues: 2667 sheet: -0.31 (0.18), residues: 791 loop : -1.16 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP w 213 HIS 0.014 0.001 HIS P 79 PHE 0.037 0.002 PHE J 147 TYR 0.029 0.002 TYR R 53 ARG 0.012 0.001 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 544 time to evaluate : 5.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 47 residues processed: 599 average time/residue: 0.8258 time to fit residues: 843.2101 Evaluate side-chains 575 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 528 time to evaluate : 5.324 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.6844 time to fit residues: 66.6999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 717 optimal weight: 50.0000 chunk 83 optimal weight: 8.9990 chunk 423 optimal weight: 6.9990 chunk 543 optimal weight: 1.9990 chunk 420 optimal weight: 4.9990 chunk 626 optimal weight: 9.9990 chunk 415 optimal weight: 0.8980 chunk 741 optimal weight: 40.0000 chunk 463 optimal weight: 9.9990 chunk 451 optimal weight: 4.9990 chunk 342 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN w 27 ASN ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 527 HIS ** a 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 88543 Z= 0.304 Angle : 0.677 15.229 127020 Z= 0.344 Chirality : 0.041 0.334 15486 Planarity : 0.005 0.113 10272 Dihedral : 21.794 179.157 30036 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.14 % Favored : 95.84 % Rotamer: Outliers : 0.97 % Allowed : 16.80 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.05 % Twisted Proline : 0.37 % 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: -0.19 (0.11), residues: 6136 helix: 0.90 (0.10), residues: 2664 sheet: -0.25 (0.18), residues: 788 loop : -1.11 (0.12), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP w 213 HIS 0.013 0.001 HIS P 79 PHE 0.036 0.002 PHE f 131 TYR 0.028 0.001 TYR R 53 ARG 0.008 0.000 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 554 time to evaluate : 5.480 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: 52 outliers final: 25 residues processed: 591 average time/residue: 0.8688 time to fit residues: 876.0425 Evaluate side-chains 558 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 533 time to evaluate : 5.301 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.6236 time to fit residues: 36.8384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 458 optimal weight: 8.9990 chunk 295 optimal weight: 4.9990 chunk 442 optimal weight: 10.0000 chunk 223 optimal weight: 0.5980 chunk 145 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 471 optimal weight: 7.9990 chunk 504 optimal weight: 20.0000 chunk 366 optimal weight: 20.0000 chunk 69 optimal weight: 40.0000 chunk 582 optimal weight: 0.4980 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 27 ASN ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 115 ASN ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 527 HIS ** a 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 88543 Z= 0.349 Angle : 0.715 15.543 127020 Z= 0.362 Chirality : 0.043 0.348 15486 Planarity : 0.006 0.131 10272 Dihedral : 21.801 179.967 30036 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.68 % Favored : 95.30 % Rotamer: Outliers : 0.98 % Allowed : 17.00 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.05 % Twisted Proline : 0.37 % 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: -0.24 (0.11), residues: 6136 helix: 0.87 (0.10), residues: 2666 sheet: -0.33 (0.18), residues: 798 loop : -1.13 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP w 213 HIS 0.013 0.001 HIS P 79 PHE 0.055 0.002 PHE f 131 TYR 0.033 0.002 TYR R 53 ARG 0.010 0.001 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 533 time to evaluate : 5.488 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: 53 outliers final: 29 residues processed: 566 average time/residue: 0.8615 time to fit residues: 828.7757 Evaluate side-chains 556 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 527 time to evaluate : 5.303 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.6752 time to fit residues: 43.4580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 674 optimal weight: 10.0000 chunk 710 optimal weight: 30.0000 chunk 647 optimal weight: 0.7980 chunk 690 optimal weight: 50.0000 chunk 709 optimal weight: 20.0000 chunk 415 optimal weight: 1.9990 chunk 300 optimal weight: 0.4980 chunk 542 optimal weight: 0.5980 chunk 211 optimal weight: 0.9990 chunk 624 optimal weight: 9.9990 chunk 653 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 27 ASN W 15 ASN ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 527 HIS ** a 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 88543 Z= 0.147 Angle : 0.591 13.981 127020 Z= 0.304 Chirality : 0.037 0.308 15486 Planarity : 0.004 0.112 10272 Dihedral : 21.635 179.953 30036 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 0.37 % Allowed : 17.54 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.05 % Twisted Proline : 0.37 % 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: 0.01 (0.11), residues: 6136 helix: 1.07 (0.10), residues: 2664 sheet: -0.26 (0.18), residues: 825 loop : -0.96 (0.12), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP w 213 HIS 0.011 0.001 HIS P 79 PHE 0.083 0.001 PHE f 131 TYR 0.043 0.001 TYR R 53 ARG 0.023 0.000 ARG O 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 578 time to evaluate : 5.377 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: 20 outliers final: 11 residues processed: 589 average time/residue: 0.8335 time to fit residues: 835.7129 Evaluate side-chains 558 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 547 time to evaluate : 5.487 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6166 time to fit residues: 20.0239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 688 optimal weight: 0.5980 chunk 453 optimal weight: 3.9990 chunk 730 optimal weight: 5.9990 chunk 445 optimal weight: 0.9990 chunk 346 optimal weight: 40.0000 chunk 507 optimal weight: 6.9990 chunk 766 optimal weight: 10.0000 chunk 705 optimal weight: 40.0000 chunk 610 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 471 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 27 ASN ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 527 HIS ** a 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 88543 Z= 0.257 Angle : 0.650 14.690 127020 Z= 0.331 Chirality : 0.040 0.332 15486 Planarity : 0.005 0.113 10272 Dihedral : 21.624 179.573 30036 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.96 % Rotamer: Outliers : 0.22 % Allowed : 18.12 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.05 % Twisted Proline : 0.37 % 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: -0.01 (0.11), residues: 6136 helix: 1.03 (0.10), residues: 2671 sheet: -0.21 (0.18), residues: 801 loop : -0.98 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP w 213 HIS 0.012 0.001 HIS P 79 PHE 0.034 0.002 PHE f 131 TYR 0.042 0.001 TYR R 53 ARG 0.015 0.000 ARG O 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12272 Ramachandran restraints generated. 6136 Oldfield, 0 Emsley, 6136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 549 time to evaluate : 5.512 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: 12 outliers final: 6 residues processed: 555 average time/residue: 0.8474 time to fit residues: 798.2897 Evaluate side-chains 545 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 539 time to evaluate : 5.431 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.6401 time to fit residues: 13.9802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 374 optimal weight: 6.9990 chunk 484 optimal weight: 6.9990 chunk 649 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 chunk 562 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 611 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 627 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 27 ASN W 15 ASN ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 GLN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 527 HIS K 999 HIS ** a 134 HIS ** 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 = 0.4405 r_free = 0.4405 target = 0.166448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.153511 restraints weight = 143334.831| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 0.65 r_work: 0.4051 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4026 r_free = 0.4026 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4026 r_free = 0.4026 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 88543 Z= 0.386 Angle : 0.742 15.287 127020 Z= 0.373 Chirality : 0.044 0.358 15486 Planarity : 0.006 0.139 10272 Dihedral : 21.726 179.784 30036 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.68 % Favored : 95.30 % Rotamer: Outliers : 0.22 % Allowed : 18.43 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.05 % Twisted Proline : 0.37 % Twisted General : 0.03 % 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: -0.17 (0.11), residues: 6136 helix: 0.91 (0.10), residues: 2670 sheet: -0.26 (0.18), residues: 794 loop : -1.09 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP w 213 HIS 0.012 0.001 HIS P 79 PHE 0.035 0.002 PHE J 147 TYR 0.040 0.002 TYR R 53 ARG 0.011 0.001 ARG O 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16502.94 seconds wall clock time: 293 minutes 59.60 seconds (17639.60 seconds total)