Starting phenix.real_space_refine on Tue Feb 20 05:26:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/02_2024/7wtt_32800_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/02_2024/7wtt_32800.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/02_2024/7wtt_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_32800/02_2024/7wtt_32800_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/02_2024/7wtt_32800_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/02_2024/7wtt_32800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/02_2024/7wtt_32800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/02_2024/7wtt_32800_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtt_32800/02_2024/7wtt_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 32.15, per 1000 atoms: 0.38 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: 30.10 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: 31.89 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: 60.52 Time building geometry restraints manager: 32.81 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: 51319 35.83 - 71.67: 4193 71.67 - 107.50: 495 107.50 - 143.33: 19 143.33 - 179.16: 24 Dihedral angle restraints: 56050 sinusoidal: 37949 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 56047 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 12.390 Check model and map are aligned: 0.930 Set scattering table: 0.560 Process input model: 230.660 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 251.600 ------------------------------------------------------------------------------- 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 : 21.568 179.163 44322 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 : 5.290 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: Y 51 THR cc_start: 0.8116 (t) cc_final: 0.7848 (t) REVERT: a 115 MET cc_start: -0.1607 (mmt) cc_final: -0.3581 (mpp) REVERT: z 111 ARG cc_start: 0.5431 (mtt180) cc_final: 0.5188 (mmm-85) outliers start: 25 outliers final: 2 residues processed: 681 average time/residue: 0.8070 time to fit residues: 927.6095 Evaluate side-chains 539 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 537 time to evaluate : 5.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 343 VAL Chi-restraints excluded: chain u residue 679 ILE 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 88543 Z= 0.403 Angle : 0.768 16.180 127020 Z= 0.387 Chirality : 0.045 0.353 15486 Planarity : 0.006 0.133 10272 Dihedral : 22.847 179.374 31475 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.14 % Rotamer: Outliers : 1.32 % Allowed : 8.98 % Favored : 89.70 % 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: -0.76 (0.10), residues: 6136 helix: 0.26 (0.10), residues: 2686 sheet: -0.43 (0.18), residues: 791 loop : -1.26 (0.11), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP u 133 HIS 0.017 0.002 HIS P 79 PHE 0.039 0.002 PHE J 147 TYR 0.033 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 623 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 552 time to evaluate : 6.287 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: G 85 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7969 (ttp80) REVERT: I 109 TYR cc_start: 0.6425 (m-80) cc_final: 0.6214 (m-80) REVERT: q 179 THR cc_start: 0.3136 (p) cc_final: 0.2921 (p) REVERT: z 111 ARG cc_start: 0.5679 (mtt180) cc_final: 0.5371 (mmm-85) REVERT: z 222 MET cc_start: 0.0057 (mmt) cc_final: -0.0583 (mmt) outliers start: 71 outliers final: 49 residues processed: 592 average time/residue: 0.7909 time to fit residues: 800.4279 Evaluate side-chains 579 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 530 time to evaluate : 5.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain w residue 220 THR Chi-restraints excluded: chain w residue 301 THR Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 343 VAL Chi-restraints excluded: chain u residue 344 LEU Chi-restraints excluded: chain u residue 488 VAL Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 96 TYR Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain q residue 160 VAL Chi-restraints excluded: chain q residue 161 LEU Chi-restraints excluded: chain q residue 189 VAL Chi-restraints excluded: chain K residue 423 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 388 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 581 optimal weight: 30.0000 chunk 475 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 699 optimal weight: 0.0980 chunk 755 optimal weight: 8.9990 chunk 623 optimal weight: 10.0000 chunk 693 optimal weight: 20.0000 chunk 238 optimal weight: 6.9990 chunk 561 optimal weight: 0.4980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 ASN ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 11 HIS ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 GLN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 ASN I 165 GLN 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: 0.6438 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 88543 Z= 0.216 Angle : 0.615 14.624 127020 Z= 0.317 Chirality : 0.039 0.314 15486 Planarity : 0.005 0.113 10272 Dihedral : 22.711 179.316 31475 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 1.69 % Allowed : 11.68 % Favored : 86.63 % 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: -0.37 (0.10), residues: 6136 helix: 0.66 (0.10), residues: 2686 sheet: -0.35 (0.18), residues: 806 loop : -1.09 (0.12), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP w 213 HIS 0.013 0.001 HIS P 79 PHE 0.024 0.001 PHE J 147 TYR 0.018 0.001 TYR J 35 ARG 0.010 0.000 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 658 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 567 time to evaluate : 5.234 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: G 85 ARG cc_start: 0.8276 (ttp80) cc_final: 0.8057 (ttt-90) REVERT: G 91 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6905 (pt0) REVERT: Y 51 THR cc_start: 0.8077 (t) cc_final: 0.7867 (t) REVERT: u 120 GLN cc_start: 0.5619 (mp10) cc_final: 0.5384 (pm20) REVERT: u 595 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.7034 (m-40) REVERT: I 105 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6569 (m-30) REVERT: q 161 LEU cc_start: 0.5374 (OUTLIER) cc_final: 0.5106 (mp) REVERT: K 155 MET cc_start: 0.1587 (mmt) cc_final: -0.0939 (ptp) REVERT: z 111 ARG cc_start: 0.5547 (mtt180) cc_final: 0.5342 (mmm-85) REVERT: z 222 MET cc_start: -0.0112 (mmt) cc_final: -0.0558 (mmt) outliers start: 91 outliers final: 59 residues processed: 620 average time/residue: 0.7898 time to fit residues: 834.9261 Evaluate side-chains 602 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 539 time to evaluate : 5.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain H residue 44 ASN Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain w residue 87 THR Chi-restraints excluded: chain w residue 220 THR Chi-restraints excluded: chain w residue 321 HIS Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain u residue 202 ASP Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 343 VAL Chi-restraints excluded: chain u residue 393 VAL Chi-restraints excluded: chain u residue 488 VAL Chi-restraints excluded: chain u residue 570 VAL Chi-restraints excluded: chain u residue 595 ASN Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain O residue 32 HIS Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain r residue 106 MET Chi-restraints excluded: chain q residue 161 LEU Chi-restraints excluded: chain q residue 189 VAL Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain K residue 423 CYS Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain a residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 691 optimal weight: 30.0000 chunk 525 optimal weight: 0.7980 chunk 363 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 chunk 333 optimal weight: 10.0000 chunk 469 optimal weight: 9.9990 chunk 702 optimal weight: 9.9990 chunk 743 optimal weight: 50.0000 chunk 366 optimal weight: 10.0000 chunk 665 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 overall best weight: 5.3386 ------------------------------------------------------------------------------- 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** H 44 ASN H 68 GLN X 46 HIS W 15 ASN ** t 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 137 GLN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN q 132 ASN K 527 HIS K1127 GLN ** a 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 88543 Z= 0.395 Angle : 0.736 15.337 127020 Z= 0.370 Chirality : 0.044 0.359 15486 Planarity : 0.006 0.144 10272 Dihedral : 22.739 179.645 31475 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.40 % Favored : 95.58 % Rotamer: Outliers : 2.38 % Allowed : 12.77 % Favored : 84.85 % 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: -0.36 (0.11), residues: 6136 helix: 0.72 (0.10), residues: 2680 sheet: -0.33 (0.18), residues: 791 loop : -1.16 (0.11), residues: 2665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP w 213 HIS 0.015 0.001 HIS P 79 PHE 0.037 0.002 PHE J 147 TYR 0.026 0.002 TYR I 198 ARG 0.012 0.001 ARG E 30 *********************** 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 677 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 549 time to evaluate : 5.301 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: F 160 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: G 91 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6863 (pt0) REVERT: u 120 GLN cc_start: 0.5454 (mp10) cc_final: 0.5225 (pm20) REVERT: u 595 ASN cc_start: 0.7460 (OUTLIER) cc_final: 0.7157 (m-40) REVERT: O 37 PHE cc_start: 0.5723 (OUTLIER) cc_final: 0.5504 (p90) REVERT: I 105 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6633 (m-30) REVERT: I 109 TYR cc_start: 0.6558 (m-80) cc_final: 0.6279 (m-80) REVERT: q 161 LEU cc_start: 0.5466 (OUTLIER) cc_final: 0.5123 (mp) REVERT: z 111 ARG cc_start: 0.5738 (mtt180) cc_final: 0.5420 (mmm-85) REVERT: z 222 MET cc_start: -0.0084 (mmt) cc_final: -0.0744 (mmt) outliers start: 128 outliers final: 99 residues processed: 630 average time/residue: 0.7795 time to fit residues: 841.6142 Evaluate side-chains 634 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 529 time to evaluate : 5.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain H residue 44 ASN Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 198 THR Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain w residue 87 THR Chi-restraints excluded: chain w residue 220 THR Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain u residue 202 ASP Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 343 VAL Chi-restraints excluded: chain u residue 344 LEU Chi-restraints excluded: chain u residue 393 VAL Chi-restraints excluded: chain u residue 488 VAL Chi-restraints excluded: chain u residue 562 VAL Chi-restraints excluded: chain u residue 570 VAL Chi-restraints excluded: chain u residue 595 ASN Chi-restraints excluded: chain u residue 596 MET Chi-restraints excluded: chain u residue 630 SER Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 790 LEU Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain O residue 32 HIS Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 138 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain r residue 106 MET Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 149 LEU Chi-restraints excluded: chain q residue 161 LEU Chi-restraints excluded: chain q residue 189 VAL Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain q residue 273 THR Chi-restraints excluded: chain K residue 423 CYS Chi-restraints excluded: chain K residue 917 VAL Chi-restraints excluded: chain K residue 1242 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 276 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 619 optimal weight: 8.9990 chunk 421 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 553 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 chunk 634 optimal weight: 50.0000 chunk 513 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 379 optimal weight: 0.4980 chunk 667 optimal weight: 50.0000 chunk 187 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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** H 44 ASN H 68 GLN H 76 GLN x 110 ASN X 97 ASN w 212 ASN u 131 HIS ** 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 338 HIS K 527 HIS ** a 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 88543 Z= 0.237 Angle : 0.624 14.727 127020 Z= 0.320 Chirality : 0.039 0.317 15486 Planarity : 0.005 0.112 10272 Dihedral : 22.658 179.792 31475 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 2.30 % Allowed : 14.11 % Favored : 83.59 % 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: -0.17 (0.11), residues: 6136 helix: 0.90 (0.10), residues: 2681 sheet: -0.28 (0.18), residues: 799 loop : -1.07 (0.12), residues: 2656 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 0.028 0.001 PHE w 364 TYR 0.022 0.001 TYR I 198 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 692 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 568 time to evaluate : 5.144 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: E 145 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7652 (mtt90) REVERT: G 91 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6937 (pt0) REVERT: u 401 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: u 595 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.7096 (m-40) REVERT: u 596 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7553 (mtm) REVERT: u 648 MET cc_start: 0.7900 (ppp) cc_final: 0.7233 (ppp) REVERT: I 56 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.5547 (tpp-160) REVERT: I 105 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6532 (m-30) REVERT: z 111 ARG cc_start: 0.5790 (mtt180) cc_final: 0.5526 (mmm-85) outliers start: 124 outliers final: 88 residues processed: 649 average time/residue: 0.7976 time to fit residues: 885.7955 Evaluate side-chains 642 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 547 time to evaluate : 5.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain H residue 44 ASN Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain w residue 87 THR Chi-restraints excluded: chain w residue 220 THR Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain u residue 68 VAL Chi-restraints excluded: chain u residue 202 ASP Chi-restraints excluded: chain u residue 282 THR Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 343 VAL Chi-restraints excluded: chain u residue 344 LEU Chi-restraints excluded: chain u residue 393 VAL Chi-restraints excluded: chain u residue 401 GLN Chi-restraints excluded: chain u residue 488 VAL Chi-restraints excluded: chain u residue 570 VAL Chi-restraints excluded: chain u residue 595 ASN Chi-restraints excluded: chain u residue 596 MET Chi-restraints excluded: chain u residue 636 ASP Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain O residue 32 HIS Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain r residue 106 MET Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 149 LEU Chi-restraints excluded: chain q residue 189 VAL Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain K residue 423 CYS Chi-restraints excluded: chain K residue 1002 MET Chi-restraints excluded: chain K residue 1242 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 276 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 250 optimal weight: 8.9990 chunk 669 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 436 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 744 optimal weight: 8.9990 chunk 617 optimal weight: 8.9990 chunk 344 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 246 optimal weight: 9.9990 chunk 390 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN H 44 ASN H 76 GLN x 110 ASN w 27 ASN u 190 GLN u 241 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** ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 88543 Z= 0.514 Angle : 0.837 15.745 127020 Z= 0.413 Chirality : 0.049 0.386 15486 Planarity : 0.007 0.158 10272 Dihedral : 22.779 179.489 31475 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.91 % Favored : 95.08 % Rotamer: Outliers : 3.23 % Allowed : 14.61 % Favored : 82.16 % 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: -0.40 (0.11), residues: 6136 helix: 0.72 (0.10), residues: 2672 sheet: -0.31 (0.18), residues: 782 loop : -1.23 (0.11), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP w 213 HIS 0.015 0.002 HIS P 79 PHE 0.040 0.002 PHE J 147 TYR 0.027 0.002 TYR I 198 ARG 0.015 0.001 ARG I 47 *********************** 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 713 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 539 time to evaluate : 5.212 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: E 126 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8009 (t) REVERT: F 160 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: G 91 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6845 (pt0) REVERT: u 401 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: u 595 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7284 (m-40) REVERT: O 37 PHE cc_start: 0.5678 (OUTLIER) cc_final: 0.5308 (p90) REVERT: L 24 LEU cc_start: 0.4450 (OUTLIER) cc_final: 0.3881 (mt) REVERT: I 56 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.5742 (tpp-160) REVERT: q 179 THR cc_start: 0.3612 (p) cc_final: 0.3361 (p) REVERT: z 111 ARG cc_start: 0.5807 (mtt180) cc_final: 0.5469 (mmm-85) outliers start: 174 outliers final: 129 residues processed: 665 average time/residue: 0.7711 time to fit residues: 881.9008 Evaluate side-chains 662 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 525 time to evaluate : 5.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 198 THR Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain w residue 87 THR Chi-restraints excluded: chain w residue 220 THR Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain u residue 68 VAL Chi-restraints excluded: chain u residue 143 LEU Chi-restraints excluded: chain u residue 202 ASP Chi-restraints excluded: chain u residue 258 VAL Chi-restraints excluded: chain u residue 282 THR Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 343 VAL Chi-restraints excluded: chain u residue 344 LEU Chi-restraints excluded: chain u residue 393 VAL Chi-restraints excluded: chain u residue 401 GLN Chi-restraints excluded: chain u residue 488 VAL Chi-restraints excluded: chain u residue 562 VAL Chi-restraints excluded: chain u residue 570 VAL Chi-restraints excluded: chain u residue 595 ASN Chi-restraints excluded: chain u residue 596 MET Chi-restraints excluded: chain u residue 630 SER Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 790 LEU Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain O residue 32 HIS Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 138 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain r residue 106 MET Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 149 LEU Chi-restraints excluded: chain q residue 160 VAL Chi-restraints excluded: chain q residue 189 VAL Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain q residue 273 THR Chi-restraints excluded: chain K residue 244 PHE Chi-restraints excluded: chain K residue 423 CYS Chi-restraints excluded: chain K residue 1002 MET Chi-restraints excluded: chain K residue 1242 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain f residue 139 HIS Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 238 GLU Chi-restraints excluded: chain a residue 276 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 717 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 423 optimal weight: 8.9990 chunk 543 optimal weight: 1.9990 chunk 420 optimal weight: 0.9980 chunk 626 optimal weight: 10.0000 chunk 415 optimal weight: 0.4980 chunk 741 optimal weight: 30.0000 chunk 463 optimal weight: 7.9990 chunk 451 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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** H 44 ASN H 68 GLN ** 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** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 88543 Z= 0.277 Angle : 0.664 15.324 127020 Z= 0.338 Chirality : 0.041 0.329 15486 Planarity : 0.005 0.113 10272 Dihedral : 22.694 178.628 31475 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.04 % Rotamer: Outliers : 2.90 % Allowed : 15.48 % Favored : 81.62 % 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: 0.90 (0.10), residues: 2668 sheet: -0.27 (0.18), residues: 785 loop : -1.12 (0.12), residues: 2683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP w 213 HIS 0.012 0.001 HIS P 79 PHE 0.031 0.002 PHE f 131 TYR 0.023 0.001 TYR I 198 ARG 0.009 0.000 ARG O 149 *********************** 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 708 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 552 time to evaluate : 5.244 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: F 160 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: G 91 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6927 (pt0) REVERT: X 97 ASN cc_start: 0.7619 (m-40) cc_final: 0.7394 (t0) REVERT: u 401 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: u 595 ASN cc_start: 0.7435 (OUTLIER) cc_final: 0.7182 (m-40) REVERT: u 596 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7655 (mtm) REVERT: P 118 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7098 (mt-10) REVERT: L 24 LEU cc_start: 0.4440 (OUTLIER) cc_final: 0.3879 (mt) REVERT: I 56 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.5650 (tpp-160) REVERT: z 111 ARG cc_start: 0.5860 (mtt180) cc_final: 0.5529 (mmm-85) outliers start: 156 outliers final: 118 residues processed: 664 average time/residue: 0.7754 time to fit residues: 886.4465 Evaluate side-chains 660 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 535 time to evaluate : 5.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 44 ASN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 198 THR Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain w residue 87 THR Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain u residue 68 VAL Chi-restraints excluded: chain u residue 167 ASP Chi-restraints excluded: chain u residue 202 ASP Chi-restraints excluded: chain u residue 282 THR Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 343 VAL Chi-restraints excluded: chain u residue 344 LEU Chi-restraints excluded: chain u residue 393 VAL Chi-restraints excluded: chain u residue 401 GLN Chi-restraints excluded: chain u residue 488 VAL Chi-restraints excluded: chain u residue 562 VAL Chi-restraints excluded: chain u residue 570 VAL Chi-restraints excluded: chain u residue 595 ASN Chi-restraints excluded: chain u residue 596 MET Chi-restraints excluded: chain u residue 630 SER Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain u residue 693 VAL Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 790 LEU Chi-restraints excluded: chain t residue 349 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain O residue 32 HIS Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain r residue 106 MET Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 149 LEU Chi-restraints excluded: chain q residue 189 VAL Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain K residue 423 CYS Chi-restraints excluded: chain K residue 1002 MET Chi-restraints excluded: chain K residue 1242 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 238 GLU Chi-restraints excluded: chain a residue 276 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 458 optimal weight: 9.9990 chunk 295 optimal weight: 0.9990 chunk 442 optimal weight: 7.9990 chunk 223 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 471 optimal weight: 0.9990 chunk 504 optimal weight: 0.2980 chunk 366 optimal weight: 6.9990 chunk 69 optimal weight: 40.0000 chunk 582 optimal weight: 20.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- 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** ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 44 ASN ** 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** J 27 GLN ** r 6 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 88543 Z= 0.277 Angle : 0.665 14.947 127020 Z= 0.339 Chirality : 0.041 0.328 15486 Planarity : 0.005 0.113 10272 Dihedral : 22.640 178.934 31475 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.40 % Favored : 95.58 % Rotamer: Outliers : 2.95 % Allowed : 15.67 % Favored : 81.38 % 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: -0.16 (0.11), residues: 6136 helix: 0.95 (0.10), residues: 2664 sheet: -0.30 (0.18), residues: 792 loop : -1.10 (0.12), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP w 213 HIS 0.012 0.001 HIS P 79 PHE 0.047 0.002 PHE f 131 TYR 0.027 0.001 TYR f 105 ARG 0.010 0.000 ARG I 92 *********************** 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 704 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 545 time to evaluate : 5.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 160 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: G 91 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6934 (pt0) REVERT: u 401 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: u 595 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.7152 (m-40) REVERT: u 596 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7637 (mtm) REVERT: O 106 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7188 (mmtp) REVERT: I 23 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7488 (pttt) REVERT: I 56 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.5585 (tpp-160) REVERT: K 155 MET cc_start: 0.1285 (mmt) cc_final: -0.1227 (ptp) REVERT: z 111 ARG cc_start: 0.5877 (mtt180) cc_final: 0.5510 (mmm-85) outliers start: 159 outliers final: 132 residues processed: 658 average time/residue: 0.8300 time to fit residues: 938.6433 Evaluate side-chains 673 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 533 time to evaluate : 5.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 44 ASN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 198 THR Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain w residue 87 THR Chi-restraints excluded: chain w residue 204 PHE Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain u residue 68 VAL Chi-restraints excluded: chain u residue 167 ASP Chi-restraints excluded: chain u residue 202 ASP Chi-restraints excluded: chain u residue 282 THR Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 343 VAL Chi-restraints excluded: chain u residue 344 LEU Chi-restraints excluded: chain u residue 393 VAL Chi-restraints excluded: chain u residue 401 GLN Chi-restraints excluded: chain u residue 488 VAL Chi-restraints excluded: chain u residue 562 VAL Chi-restraints excluded: chain u residue 570 VAL Chi-restraints excluded: chain u residue 595 ASN Chi-restraints excluded: chain u residue 596 MET Chi-restraints excluded: chain u residue 630 SER Chi-restraints excluded: chain u residue 636 ASP Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 679 ILE Chi-restraints excluded: chain u residue 693 VAL Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 790 LEU Chi-restraints excluded: chain t residue 349 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain O residue 32 HIS Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain r residue 106 MET Chi-restraints excluded: chain r residue 115 ASN Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 149 LEU Chi-restraints excluded: chain q residue 189 VAL Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain K residue 423 CYS Chi-restraints excluded: chain K residue 1002 MET Chi-restraints excluded: chain K residue 1242 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 238 GLU Chi-restraints excluded: chain a residue 276 TYR 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: 40.0000 chunk 647 optimal weight: 0.0040 chunk 690 optimal weight: 50.0000 chunk 709 optimal weight: 7.9990 chunk 415 optimal weight: 0.9990 chunk 300 optimal weight: 0.7980 chunk 542 optimal weight: 1.9990 chunk 211 optimal weight: 0.0870 chunk 624 optimal weight: 10.0000 chunk 653 optimal weight: 7.9990 overall best weight: 0.7774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 HIS ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 ASN ** 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** ** r 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 115 ASN 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: 0.6388 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 88543 Z= 0.139 Angle : 0.584 13.613 127020 Z= 0.301 Chirality : 0.036 0.269 15486 Planarity : 0.004 0.112 10272 Dihedral : 22.498 179.444 31475 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.20 % Favored : 96.79 % Rotamer: Outliers : 1.78 % Allowed : 16.84 % Favored : 81.38 % 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: 0.06 (0.11), residues: 6136 helix: 1.10 (0.10), residues: 2665 sheet: -0.26 (0.18), residues: 809 loop : -0.92 (0.12), residues: 2662 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 0.036 0.001 PHE f 131 TYR 0.048 0.001 TYR R 53 ARG 0.011 0.000 ARG r 19 *********************** 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 664 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 568 time to evaluate : 5.969 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: E 145 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7486 (mtt90) REVERT: G 85 ARG cc_start: 0.8215 (ttp80) cc_final: 0.8001 (ttt-90) REVERT: Y 51 THR cc_start: 0.8065 (t) cc_final: 0.7804 (t) REVERT: u 648 MET cc_start: 0.7666 (ppp) cc_final: 0.7128 (ppp) REVERT: K 935 MET cc_start: -0.0101 (pmm) cc_final: -0.0887 (pmm) REVERT: z 111 ARG cc_start: 0.5560 (mtt180) cc_final: 0.5310 (mmm-85) outliers start: 96 outliers final: 77 residues processed: 629 average time/residue: 0.7926 time to fit residues: 853.4933 Evaluate side-chains 622 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 544 time to evaluate : 5.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 97 ASN Chi-restraints excluded: chain w residue 87 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain u residue 202 ASP Chi-restraints excluded: chain u residue 282 THR Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 343 VAL Chi-restraints excluded: chain u residue 393 VAL Chi-restraints excluded: chain u residue 482 GLU Chi-restraints excluded: chain u residue 562 VAL Chi-restraints excluded: chain u residue 570 VAL Chi-restraints excluded: chain u residue 630 SER Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain O residue 32 HIS Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain r residue 106 MET Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 83 ILE Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 149 LEU Chi-restraints excluded: chain q residue 189 VAL Chi-restraints excluded: chain K residue 423 CYS Chi-restraints excluded: chain K residue 1002 MET Chi-restraints excluded: chain K residue 1242 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 128 HIS Chi-restraints excluded: chain a residue 238 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 688 optimal weight: 40.0000 chunk 453 optimal weight: 6.9990 chunk 730 optimal weight: 7.9990 chunk 445 optimal weight: 5.9990 chunk 346 optimal weight: 30.0000 chunk 507 optimal weight: 5.9990 chunk 766 optimal weight: 9.9990 chunk 705 optimal weight: 8.9990 chunk 610 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 471 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN X 97 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** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 88543 Z= 0.445 Angle : 0.783 15.237 127020 Z= 0.390 Chirality : 0.046 0.372 15486 Planarity : 0.006 0.164 10272 Dihedral : 22.616 178.438 31473 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.60 % Favored : 95.39 % Rotamer: Outliers : 1.76 % Allowed : 17.02 % Favored : 81.21 % 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: 0.90 (0.10), residues: 2667 sheet: -0.28 (0.18), residues: 787 loop : -1.11 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP w 213 HIS 0.013 0.001 HIS P 79 PHE 0.035 0.002 PHE J 147 TYR 0.033 0.002 TYR T 65 ARG 0.012 0.001 ARG I 92 ********************** 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 623 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 528 time to evaluate : 5.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 91 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7019 (pt0) REVERT: J 21 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6164 (pt0) REVERT: K 935 MET cc_start: -0.0452 (pmm) cc_final: -0.1184 (pmm) REVERT: z 111 ARG cc_start: 0.5841 (mtt180) cc_final: 0.5421 (mmm-85) REVERT: z 181 MET cc_start: 0.0146 (ppp) cc_final: -0.0169 (pmm) outliers start: 95 outliers final: 83 residues processed: 593 average time/residue: 0.8010 time to fit residues: 821.6666 Evaluate side-chains 603 residues out of total 5421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 518 time to evaluate : 5.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 97 ASN Chi-restraints excluded: chain X residue 139 GLU Chi-restraints excluded: chain w residue 87 THR Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain u residue 202 ASP Chi-restraints excluded: chain u residue 282 THR Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 343 VAL Chi-restraints excluded: chain u residue 393 VAL Chi-restraints excluded: chain u residue 482 GLU Chi-restraints excluded: chain u residue 562 VAL Chi-restraints excluded: chain u residue 630 SER Chi-restraints excluded: chain u residue 636 ASP Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 693 VAL Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain O residue 32 HIS Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 21 GLU Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain r residue 106 MET Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 189 VAL Chi-restraints excluded: chain K residue 423 CYS Chi-restraints excluded: chain K residue 1002 MET Chi-restraints excluded: chain K residue 1242 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 238 GLU Chi-restraints excluded: chain a residue 276 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 374 optimal weight: 3.9990 chunk 484 optimal weight: 3.9990 chunk 649 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 562 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 611 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 627 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 HIS ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 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** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.168006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.154843 restraints weight = 143413.393| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 0.54 r_work: 0.4072 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.4043 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 88543 Z= 0.231 Angle : 0.640 14.823 127020 Z= 0.328 Chirality : 0.039 0.315 15486 Planarity : 0.005 0.113 10272 Dihedral : 22.560 179.534 31473 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.90 % Favored : 96.09 % Rotamer: Outliers : 1.65 % Allowed : 17.32 % Favored : 81.03 % 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: -0.10 (0.11), residues: 6136 helix: 0.96 (0.10), residues: 2669 sheet: -0.28 (0.18), residues: 805 loop : -1.02 (0.12), residues: 2662 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 0.027 0.001 PHE J 147 TYR 0.033 0.001 TYR T 65 ARG 0.011 0.000 ARG I 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16595.11 seconds wall clock time: 295 minutes 1.86 seconds (17701.86 seconds total)