Starting phenix.real_space_refine on Tue Feb 20 13:21:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtw_32803/02_2024/7wtw_32803_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtw_32803/02_2024/7wtw_32803.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtw_32803/02_2024/7wtw_32803_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtw_32803/02_2024/7wtw_32803_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtw_32803/02_2024/7wtw_32803_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtw_32803/02_2024/7wtw_32803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtw_32803/02_2024/7wtw_32803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtw_32803/02_2024/7wtw_32803_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtw_32803/02_2024/7wtw_32803_updated.pdb" } resolution = 3.2 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= 0.001 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 2 6.06 5 P 1586 5.49 5 S 250 5.16 5 C 48960 2.51 5 N 15895 2.21 5 O 20454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 87147 Number of models: 1 Model: "" Number of chains: 39 Chain: "2" Number of atoms: 33870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1586, 33870 Classifications: {'RNA': 1586} Modifications used: {'rna2p': 1, 'rna2p_pur': 122, 'rna2p_pyr': 98, 'rna3p_pur': 718, 'rna3p_pyr': 647} Link IDs: {'rna2p': 220, 'rna3p': 1365} 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: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2617 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 17, '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: "t" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 931 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 2 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: 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: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1571 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain: "K" Number of atoms: 7707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7707 Classifications: {'peptide': 993} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 944} Chain breaks: 9 Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 2 Chain: "f" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 465 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain breaks: 1 Chain: "z" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 416 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "C" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1674 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "V" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "y" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2091 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 250} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "y" 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 86507 SG CYS y 270 110.018 167.422 152.594 1.00 22.96 S ATOM 86527 SG CYS y 273 113.171 166.882 154.366 1.00 25.13 S ATOM 86624 SG CYS y 285 113.279 168.676 151.024 1.00 23.37 S ATOM 86646 SG CYS y 288 112.542 164.953 151.110 1.00 24.19 S Time building chain proxies: 33.76, per 1000 atoms: 0.39 Number of scatterers: 87147 At special positions: 0 Unit cell: (256.278, 252.042, 201.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 250 16.00 P 1586 15.00 O 20454 8.00 N 15895 7.00 C 48960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.61 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN y 500 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 270 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 273 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 285 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 288 " Number of angles added : 6 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12548 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 254 helices and 50 sheets defined 40.0% alpha, 12.0% beta 526 base pairs and 871 stacking pairs defined. Time for finding SS restraints: 35.66 Creating SS restraints... Processing helix chain 'R' and resid 7 through 19 Processing helix chain 'R' and resid 28 through 38 Processing helix chain 'R' and resid 44 through 62 Processing helix chain 'R' and resid 66 through 82 Processing helix chain 'b' and resid 12 through 17 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 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 176 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 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 38 through 40 No H-bonds generated for 'chain 'E' and resid 38 through 40' Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 58 through 66 Processing helix chain 'E' and resid 116 through 120 removed outlier: 3.692A pdb=" N LYS E 120 " --> pdb=" O GLU E 117 " (cutoff:3.500A) 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 68 through 76 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 87 through 104 Processing helix chain 'F' and resid 108 through 118 Processing helix chain 'F' and resid 143 through 161 Processing helix chain 'F' and resid 169 through 182 Processing helix chain 'F' and resid 188 through 203 Processing helix chain 'H' and resid 18 through 33 Processing helix chain 'H' and resid 66 through 74 removed outlier: 5.162A pdb=" N LYS H 70 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER H 71 " --> pdb=" O GLN H 68 " (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 170 through 181 Processing helix chain 'G' and resid 21 through 26 removed outlier: 3.949A pdb=" N ARG G 25 " --> pdb=" O GLU G 21 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 21 through 26' Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'G' and resid 153 through 156 Processing helix chain 'G' and resid 182 through 228 Processing helix chain 'Z' and resid 52 through 64 removed outlier: 3.606A pdb=" N VAL Z 62 " --> pdb=" O LEU Z 58 " (cutoff:3.500A) Proline residue: Z 63 - end of helix Processing helix chain 'Z' and resid 70 through 77 Processing helix chain 'Z' and resid 81 through 94 Processing helix chain 'Y' and resid 37 through 48 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 79 through 85 Processing helix chain 'Y' and resid 88 through 93 Processing helix chain 'Y' and resid 104 through 114 Processing helix chain 'Y' and resid 120 through 124 Processing helix chain 'x' and resid 82 through 90 removed outlier: 3.695A pdb=" N TYR x 85 " --> pdb=" O ALA x 82 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N THR x 86 " --> pdb=" O ASN x 83 " (cutoff:3.500A) Proline residue: x 87 - end of helix Processing helix chain 'x' and resid 93 through 100 Proline residue: x 98 - end of helix Processing helix chain 'x' and resid 130 through 142 Processing helix chain 'x' and resid 146 through 154 Processing helix chain 'x' and resid 174 through 184 Processing helix chain 'x' and resid 186 through 198 removed outlier: 6.195A pdb=" N THR x 190 " --> pdb=" O GLY x 187 " (cutoff:3.500A) Processing helix chain 'x' and resid 215 through 230 Processing helix chain 'x' and resid 234 through 246 Processing helix chain 'X' and resid 10 through 23 removed outlier: 4.253A pdb=" N HIS X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 31 Processing helix chain 'X' and resid 88 through 93 removed outlier: 3.726A pdb=" N ASN X 92 " --> pdb=" O ASP X 88 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE X 93 " --> pdb=" O GLY X 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 88 through 93' Processing helix chain 'X' and resid 130 through 134 Processing helix chain 'w' and resid 19 through 27 Processing helix chain 'w' and resid 52 through 71 Processing helix chain 'w' and resid 143 through 166 Processing helix chain 'w' and resid 180 through 194 removed outlier: 3.871A pdb=" N LYS w 194 " --> pdb=" O GLU w 190 " (cutoff:3.500A) Processing helix chain 'w' and resid 202 through 206 Processing helix chain 'w' and resid 213 through 220 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 238 Processing helix chain 'w' and resid 243 through 252 Processing helix chain 'w' and resid 254 through 265 Processing helix chain 'w' and resid 270 through 281 removed outlier: 3.564A pdb=" N PHE w 281 " --> pdb=" O LYS w 277 " (cutoff:3.500A) 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 331 Processing helix chain 'w' and resid 338 through 347 Processing helix chain 'w' and resid 354 through 367 removed outlier: 4.696A pdb=" N PHE w 367 " --> pdb=" O HIS w 363 " (cutoff:3.500A) Processing helix chain 'w' and resid 376 through 388 Processing helix chain 'w' and resid 395 through 407 Processing helix chain 'w' and resid 413 through 422 Processing helix chain 't' and resid 267 through 269 No H-bonds generated for 'chain 't' and resid 267 through 269' Processing helix chain 't' and resid 350 through 356 removed outlier: 3.962A pdb=" N CYS t 354 " --> pdb=" O CYS t 350 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER t 355 " --> pdb=" O GLU t 351 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR t 356 " --> pdb=" O SER t 352 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 350 through 356' Processing helix chain 't' and resid 427 through 468 Processing helix chain 'W' and resid 6 through 19 Processing helix chain 'W' and resid 32 through 44 removed outlier: 3.735A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 93 Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'u' and resid 50 through 73 Processing helix chain 'u' and resid 96 through 102 Processing helix chain 'u' and resid 143 through 150 Processing helix chain 'u' and resid 168 through 180 Processing helix chain 'u' and resid 197 through 213 removed outlier: 4.400A pdb=" N LYS u 213 " --> pdb=" O LYS u 209 " (cutoff:3.500A) Processing helix chain 'u' and resid 226 through 237 Processing helix chain 'u' and resid 399 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 526 Processing helix chain 'u' and resid 533 through 545 Processing helix chain 'u' and resid 567 through 574 removed outlier: 3.928A pdb=" N ARG u 574 " --> pdb=" O GLU u 571 " (cutoff:3.500A) Processing helix chain 'u' and resid 720 through 727 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 34 through 36 No H-bonds generated for 'chain 'T' and resid 34 through 36' 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 32 removed outlier: 3.995A pdb=" N ILE S 30 " --> pdb=" O ILE S 26 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA S 32 " --> pdb=" O PHE S 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 26 through 32' Processing helix chain 'S' and resid 38 through 47 Processing helix chain 'S' and resid 61 through 72 Processing helix chain 'S' and resid 74 through 77 Processing helix chain 'S' and resid 81 through 83 No H-bonds generated for 'chain 'S' and resid 81 through 83' Processing helix chain 'S' and resid 102 through 116 Processing helix chain 'S' and resid 120 through 128 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 46 through 51 removed outlier: 4.518A pdb=" N TYR Q 49 " --> pdb=" O THR Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 58 Processing helix chain 'Q' and resid 62 through 65 removed outlier: 3.914A pdb=" N GLY Q 65 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 62 through 65' Processing helix chain 'Q' and resid 77 through 98 Processing helix chain 'Q' and resid 102 through 115 Processing helix chain 'P' and resid 22 through 27 removed outlier: 3.623A pdb=" N ASP P 27 " --> pdb=" O ASP P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 46 Processing helix chain 'P' and resid 52 through 66 removed outlier: 4.056A pdb=" N GLU P 66 " --> pdb=" O LYS P 62 " (cutoff:3.500A) 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 117 through 119 No H-bonds generated for 'chain 'P' and resid 117 through 119' Processing helix chain 'O' and resid 58 through 60 No H-bonds generated for 'chain 'O' and resid 58 through 60' Processing helix chain 'O' and resid 71 through 86 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 57 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 77 Processing helix chain 'N' and resid 86 through 104 Processing helix chain 'N' and resid 109 through 131 Processing helix chain 'N' and resid 147 through 149 No H-bonds generated for 'chain 'N' and resid 147 through 149' Processing helix chain 'L' and resid 24 through 29 Processing helix chain 'L' and resid 48 through 51 No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 40 through 62 removed outlier: 3.882A pdb=" N THR J 62 " --> pdb=" O ARG J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 83 Processing helix chain 'J' and resid 94 through 98 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 193 through 205 Processing helix chain 'r' and resid 3 through 7 Processing helix chain 'r' and resid 39 through 46 removed outlier: 4.090A pdb=" N ILE r 46 " --> pdb=" O VAL r 42 " (cutoff:3.500A) Processing helix chain 'r' and resid 51 through 60 Processing helix chain 'r' and resid 78 through 88 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 94 Processing helix chain 'q' and resid 105 through 107 No H-bonds generated for 'chain 'q' and resid 105 through 107' Processing helix chain 'q' and resid 138 through 152 Processing helix chain 'q' and resid 168 through 180 Processing helix chain 'K' and resid 109 through 114 Processing helix chain 'K' and resid 130 through 133 No H-bonds generated for 'chain 'K' and resid 130 through 133' Processing helix chain 'K' and resid 138 through 140 No H-bonds generated for 'chain 'K' and resid 138 through 140' Processing helix chain 'K' and resid 146 through 149 No H-bonds generated for 'chain 'K' and resid 146 through 149' 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 163 through 174 Processing helix chain 'K' and resid 180 through 204 removed outlier: 5.314A pdb=" N SER K 188 " --> pdb=" O ILE K 184 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASP K 189 " --> pdb=" O LYS K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 223 Processing helix chain 'K' and resid 233 through 245 removed outlier: 3.647A pdb=" N THR K 245 " --> pdb=" O LEU K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 264 Processing helix chain 'K' and resid 281 through 293 Processing helix chain 'K' and resid 303 through 314 Processing helix chain 'K' and resid 320 through 335 removed outlier: 4.116A pdb=" N THR K 335 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 354 Processing helix chain 'K' and resid 364 through 376 removed outlier: 4.483A pdb=" N ASP K 376 " --> pdb=" O THR K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 404 Processing helix chain 'K' and resid 406 through 424 Proline residue: K 414 - end of helix Processing helix chain 'K' and resid 429 through 445 Processing helix chain 'K' and resid 448 through 454 removed outlier: 3.575A pdb=" N MET K 451 " --> pdb=" O ALA K 448 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA K 452 " --> pdb=" O PRO K 449 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP K 453 " --> pdb=" O HIS K 450 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE K 454 " --> pdb=" O MET K 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 448 through 454' Processing helix chain 'K' and resid 464 through 479 Processing helix chain 'K' and resid 487 through 501 Processing helix chain 'K' and resid 510 through 520 Processing helix chain 'K' and resid 528 through 542 Processing helix chain 'K' and resid 544 through 550 Processing helix chain 'K' and resid 568 through 575 Processing helix chain 'K' and resid 582 through 604 removed outlier: 3.937A pdb=" N LEU K 590 " --> pdb=" O THR K 586 " (cutoff:3.500A) Proline residue: K 591 - end of helix Processing helix chain 'K' and resid 609 through 622 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 641 through 652 removed outlier: 3.524A pdb=" N ALA K 644 " --> pdb=" O LYS K 641 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ARG K 645 " --> pdb=" O GLY K 642 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR K 646 " --> pdb=" O LEU K 643 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER K 652 " --> pdb=" O MET K 649 " (cutoff:3.500A) Processing helix chain 'K' and resid 655 through 671 removed outlier: 4.449A pdb=" N VAL K 659 " --> pdb=" O PRO K 655 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR K 660 " --> pdb=" O ASP K 656 " (cutoff:3.500A) Processing helix chain 'K' and resid 676 through 697 Proline residue: K 691 - end of helix Processing helix chain 'K' and resid 710 through 723 removed outlier: 4.398A pdb=" N ILE K 723 " --> pdb=" O THR K 719 " (cutoff:3.500A) Processing helix chain 'K' and resid 726 through 741 Processing helix chain 'K' and resid 747 through 761 Processing helix chain 'K' and resid 766 through 781 Proline residue: K 778 - end of helix removed outlier: 4.867A pdb=" N GLU K 781 " --> pdb=" O ARG K 777 " (cutoff:3.500A) Processing helix chain 'K' and resid 785 through 800 Processing helix chain 'K' and resid 805 through 812 Processing helix chain 'K' and resid 814 through 823 Processing helix chain 'K' and resid 831 through 843 Proline residue: K 835 - end of helix Processing helix chain 'K' and resid 852 through 867 Proline residue: K 860 - end of helix removed outlier: 4.120A pdb=" N LYS K 867 " --> pdb=" O ILE K 863 " (cutoff:3.500A) Processing helix chain 'K' and resid 871 through 889 Processing helix chain 'K' and resid 895 through 910 removed outlier: 3.908A pdb=" N LEU K 905 " --> pdb=" O CYS K 901 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE K 906 " --> pdb=" O TYR K 902 " (cutoff:3.500A) Proline residue: K 908 - end of helix Processing helix chain 'K' and resid 914 through 930 Processing helix chain 'K' and resid 937 through 951 Processing helix chain 'K' and resid 956 through 972 Processing helix chain 'K' and resid 975 through 979 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 1022 Processing helix chain 'K' and resid 1026 through 1042 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 1103 through 1105 No H-bonds generated for 'chain 'K' and resid 1103 through 1105' Processing helix chain 'K' and resid 1125 through 1127 No H-bonds generated for 'chain 'K' and resid 1125 through 1127' Processing helix chain 'M' and resid 15 through 28 Processing helix chain 'M' and resid 35 through 43 Processing helix chain 'M' and resid 60 through 71 removed outlier: 4.048A pdb=" N LEU M 64 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU M 66 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA M 67 " --> pdb=" O LYS M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 120 through 128 Processing helix chain 'z' and resid 183 through 201 Processing helix chain 'z' and resid 210 through 224 Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 32 through 37 removed outlier: 3.785A pdb=" N GLU A 35 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLN A 36 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR A 37 " --> pdb=" O MET A 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 32 through 37' Processing helix chain 'A' and resid 51 through 66 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 81 through 94 removed outlier: 6.160A pdb=" N ARG A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.855A pdb=" N TYR A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 186 Processing helix chain 'A' and resid 199 through 202 Processing helix chain 'A' and resid 207 through 210 No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 147 through 160 Processing helix chain 'C' and resid 208 through 216 Processing helix chain 'C' and resid 233 through 248 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 265 through 268 No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'V' and resid 57 through 61 Processing helix chain 'V' and resid 65 through 76 Processing helix chain 'y' and resid 11 through 15 Processing helix chain 'y' and resid 31 through 34 No H-bonds generated for 'chain 'y' and resid 31 through 34' Processing helix chain 'y' and resid 40 through 47 removed outlier: 3.663A pdb=" N ALA y 47 " --> pdb=" O ARG y 43 " (cutoff:3.500A) Processing helix chain 'y' and resid 60 through 72 Processing helix chain 'y' and resid 81 through 97 Processing helix chain 'y' and resid 211 through 213 No H-bonds generated for 'chain 'y' and resid 211 through 213' Processing helix chain 'y' and resid 239 through 248 Processing helix chain 'y' and resid 394 through 398 removed outlier: 3.671A pdb=" N ARG y 398 " --> pdb=" O ALA y 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 394 through 398' Processing sheet with id= A, first strand: chain 'b' and resid 44 through 47 Processing sheet with id= B, first strand: chain 'B' and resid 65 through 70 removed outlier: 4.690A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 13.574A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.114A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 215 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 29 through 34 Processing sheet with id= D, first strand: chain 'c' and resid 55 through 58 removed outlier: 7.172A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'c' and resid 19 through 21 Processing sheet with id= F, first strand: chain 'E' and resid 70 through 72 Processing sheet with id= G, first strand: chain 'E' and resid 121 through 125 removed outlier: 6.242A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 146 through 148 Processing sheet with id= I, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.370A pdb=" N MET E 182 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL E 227 " --> pdb=" O MET E 182 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 123 through 129 Processing sheet with id= K, first strand: chain 'H' and resid 91 through 97 removed outlier: 3.859A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE H 45 " --> pdb=" O PRO H 65 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 185 through 189 removed outlier: 8.448A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.460A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 72 through 77 Processing sheet with id= O, first strand: chain 'G' and resid 160 through 162 Processing sheet with id= P, first strand: chain 'G' and resid 54 through 57 Processing sheet with id= Q, first strand: chain 'Z' and resid 98 through 102 removed outlier: 6.946A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Y' and resid 5 through 9 Processing sheet with id= S, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id= T, first strand: chain 'x' and resid 75 through 79 Processing sheet with id= U, first strand: chain 'x' and resid 159 through 164 Processing sheet with id= V, first strand: chain 'X' and resid 80 through 84 removed outlier: 6.146A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA X 103 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL X 122 " --> pdb=" O ALA X 103 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= X, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.401A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'u' and resid 220 through 222 removed outlier: 9.548A pdb=" N LEU u 221 " --> pdb=" O TYR u 185 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU u 187 " --> pdb=" O LEU u 221 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N SER u 137 " --> pdb=" O GLN u 120 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN u 120 " --> pdb=" O SER u 137 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'u' and resid 251 through 254 Processing sheet with id= AA, first strand: chain 'u' and resid 257 through 264 removed outlier: 7.540A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'u' and resid 629 through 631 removed outlier: 5.629A pdb=" N VAL u 597 " --> pdb=" O LEU u 684 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU u 684 " --> pdb=" O VAL u 597 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ARG u 599 " --> pdb=" O GLY u 682 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY u 682 " --> pdb=" O ARG u 599 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU u 667 " --> pdb=" O ILE u 679 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR u 681 " --> pdb=" O VAL u 665 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL u 665 " --> pdb=" O THR u 681 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLN u 670 " --> pdb=" O GLU u 613 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N GLU u 613 " --> pdb=" O GLN u 670 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'u' and resid 637 through 639 removed outlier: 6.655A pdb=" N MET u 692 " --> pdb=" O HIS u 638 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'u' and resid 710 through 713 removed outlier: 5.979A pdb=" N SER u 754 " --> pdb=" O ILE u 741 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE u 741 " --> pdb=" O SER u 754 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'T' and resid 81 through 83 Processing sheet with id= AF, first strand: chain 'T' and resid 113 through 115 Processing sheet with id= AG, first strand: chain 'S' and resid 12 through 14 Processing sheet with id= AH, first strand: chain 'Q' and resid 9 through 14 Processing sheet with id= AI, first strand: chain 'P' and resid 76 through 78 Processing sheet with id= AJ, first strand: chain 'O' and resid 52 through 57 removed outlier: 7.179A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA O 92 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N CYS O 31 " --> pdb=" O ALA O 92 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N HIS O 94 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE O 33 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS O 96 " --> pdb=" O ILE O 33 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA O 35 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG O 98 " --> pdb=" O ALA O 35 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 101 through 111 removed outlier: 6.083A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 15.438A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 17.034A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 62 through 67 Processing sheet with id= AM, first strand: chain 'I' and resid 187 through 189 removed outlier: 6.065A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 42 through 47 removed outlier: 6.299A pdb=" N HIS I 44 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA I 57 " --> pdb=" O HIS I 44 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL I 46 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TYR I 55 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'r' and resid 30 through 32 Processing sheet with id= AP, first strand: chain 'r' and resid 106 through 110 removed outlier: 4.435A pdb=" N GLU r 95 " --> pdb=" O GLU r 29 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU r 29 " --> pdb=" O GLU r 95 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N THR r 97 " --> pdb=" O ALA r 27 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA r 27 " --> pdb=" O THR r 97 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'q' and resid 184 through 190 removed outlier: 7.406A pdb=" N TYR q 77 " --> pdb=" O LEU q 57 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASP q 59 " --> pdb=" O TYR q 77 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL q 79 " --> pdb=" O ASP q 59 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP q 99 " --> pdb=" O GLY q 80 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASP q 82 " --> pdb=" O ASP q 99 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU q 101 " --> pdb=" O ASP q 82 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'M' and resid 31 through 33 removed outlier: 6.442A pdb=" N ASN M 75 " --> pdb=" O CYS M 50 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU M 52 " --> pdb=" O ASN M 75 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE M 77 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'f' and resid 133 through 135 Processing sheet with id= AT, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.202A pdb=" N LEU A 121 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 77 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL A 123 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL A 124 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 145 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 159 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS A 148 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE A 161 " --> pdb=" O CYS A 148 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'C' and resid 162 through 164 removed outlier: 6.334A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'C' and resid 184 through 188 Processing sheet with id= AW, first strand: chain 'V' and resid 32 through 36 Processing sheet with id= AX, first strand: chain 'y' and resid 262 through 270 2103 hydrogen bonds defined for protein. 5967 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1297 hydrogen bonds 1986 hydrogen bond angles 0 basepair planarities 526 basepair parallelities 871 stacking parallelities Total time for adding SS restraints: 62.41 Time building geometry restraints manager: 35.28 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: 10914 1.31 - 1.44: 33176 1.44 - 1.57: 44452 1.57 - 1.69: 3157 1.69 - 1.82: 387 Bond restraints: 92086 Sorted by residual: bond pdb=" CA GLU u 564 " pdb=" CB GLU u 564 " ideal model delta sigma weight residual 1.525 1.612 -0.087 1.47e-02 4.63e+03 3.53e+01 bond pdb=" C LYS u 727 " pdb=" N PRO u 728 " ideal model delta sigma weight residual 1.335 1.371 -0.036 9.40e-03 1.13e+04 1.46e+01 bond pdb=" C THR x 86 " pdb=" N PRO x 87 " ideal model delta sigma weight residual 1.335 1.381 -0.045 1.36e-02 5.41e+03 1.10e+01 bond pdb=" CA ASN I 64 " pdb=" CB ASN I 64 " ideal model delta sigma weight residual 1.530 1.567 -0.038 1.48e-02 4.57e+03 6.45e+00 bond pdb=" C TYR y 76 " pdb=" N PRO y 77 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.24e-02 6.50e+03 5.83e+00 ... (remaining 92081 not shown) Histogram of bond angle deviations from ideal: 95.79 - 103.71: 4751 103.71 - 111.63: 47271 111.63 - 119.55: 37295 119.55 - 127.47: 39055 127.47 - 135.39: 3509 Bond angle restraints: 131881 Sorted by residual: angle pdb=" C VAL J 137 " pdb=" N ARG J 138 " pdb=" CA ARG J 138 " ideal model delta sigma weight residual 121.54 132.18 -10.64 1.91e+00 2.74e-01 3.10e+01 angle pdb=" C GLU y 68 " pdb=" N PHE y 69 " pdb=" CA PHE y 69 " ideal model delta sigma weight residual 121.58 110.86 10.72 1.95e+00 2.63e-01 3.02e+01 angle pdb=" N GLU z 199 " pdb=" CA GLU z 199 " pdb=" CB GLU z 199 " ideal model delta sigma weight residual 110.20 117.98 -7.78 1.49e+00 4.50e-01 2.73e+01 angle pdb=" N GLU y 68 " pdb=" CA GLU y 68 " pdb=" CB GLU y 68 " ideal model delta sigma weight residual 110.16 117.87 -7.71 1.48e+00 4.57e-01 2.71e+01 angle pdb=" N VAL x 207 " pdb=" CA VAL x 207 " pdb=" C VAL x 207 " ideal model delta sigma weight residual 113.71 109.23 4.48 9.50e-01 1.11e+00 2.23e+01 ... (remaining 131876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 53557 35.99 - 71.98: 4197 71.98 - 107.97: 470 107.97 - 143.96: 22 143.96 - 179.94: 24 Dihedral angle restraints: 58270 sinusoidal: 38913 harmonic: 19357 Sorted by residual: dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 18.94 -178.94 1 1.50e+01 4.44e-03 8.53e+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 16.81 -176.81 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21865 " pdb=" C1' C 21865 " pdb=" N1 C 21865 " pdb=" C2 C 21865 " ideal model delta sinusoidal sigma weight residual -160.00 12.67 -172.67 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 58267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 15447 0.100 - 0.201: 594 0.201 - 0.301: 49 0.301 - 0.402: 5 0.402 - 0.502: 1 Chirality restraints: 16096 Sorted by residual: chirality pdb=" CB ILE X 66 " pdb=" CA ILE X 66 " pdb=" CG1 ILE X 66 " pdb=" CG2 ILE X 66 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" C1' A 2 25 " pdb=" O4' A 2 25 " pdb=" C2' A 2 25 " pdb=" N9 A 2 25 " both_signs ideal model delta sigma weight residual False 2.46 2.12 0.33 2.00e-01 2.50e+01 2.77e+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 -2.42 -0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 16093 not shown) Planarity restraints: 10849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' G7M 21639 " 0.898 2.00e-02 2.50e+03 6.00e-01 8.10e+03 pdb=" C4' G7M 21639 " -0.208 2.00e-02 2.50e+03 pdb=" O4' G7M 21639 " -0.738 2.00e-02 2.50e+03 pdb=" C3' G7M 21639 " 0.214 2.00e-02 2.50e+03 pdb=" O3' G7M 21639 " -0.918 2.00e-02 2.50e+03 pdb=" C2' G7M 21639 " 0.615 2.00e-02 2.50e+03 pdb=" O2' G7M 21639 " 0.614 2.00e-02 2.50e+03 pdb=" C1' G7M 21639 " -0.451 2.00e-02 2.50e+03 pdb=" N9 G7M 21639 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21774 " -0.009 2.00e-02 2.50e+03 2.51e-02 1.42e+01 pdb=" N1 C 21774 " 0.007 2.00e-02 2.50e+03 pdb=" C2 C 21774 " 0.061 2.00e-02 2.50e+03 pdb=" O2 C 21774 " -0.039 2.00e-02 2.50e+03 pdb=" N3 C 21774 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C 21774 " 0.007 2.00e-02 2.50e+03 pdb=" N4 C 21774 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C 21774 " -0.013 2.00e-02 2.50e+03 pdb=" C6 C 21774 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21515 " -0.006 2.00e-02 2.50e+03 2.10e-02 1.33e+01 pdb=" N9 G 21515 " -0.002 2.00e-02 2.50e+03 pdb=" C8 G 21515 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G 21515 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G 21515 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G 21515 " 0.018 2.00e-02 2.50e+03 pdb=" O6 G 21515 " -0.019 2.00e-02 2.50e+03 pdb=" N1 G 21515 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G 21515 " 0.056 2.00e-02 2.50e+03 pdb=" N2 G 21515 " -0.037 2.00e-02 2.50e+03 pdb=" N3 G 21515 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G 21515 " -0.000 2.00e-02 2.50e+03 ... (remaining 10846 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 2365 2.65 - 3.22: 71424 3.22 - 3.78: 158368 3.78 - 4.34: 209010 4.34 - 4.90: 304118 Nonbonded interactions: 745285 Sorted by model distance: nonbonded pdb=" O6 G 21302 " pdb=" O4 U 21307 " model vdw 2.092 2.432 nonbonded pdb=" O4 U 2 749 " pdb=" O6 G 2 793 " model vdw 2.100 3.040 nonbonded pdb=" O2 C 21277 " pdb=" N2 G 21322 " model vdw 2.162 2.520 nonbonded pdb=" OG SER T 59 " pdb=" OH TYR T 79 " model vdw 2.203 2.440 nonbonded pdb=" O2 C 2 216 " pdb=" N2 G 2 309 " model vdw 2.204 2.496 ... (remaining 745280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 13.020 Check model and map are aligned: 1.030 Set scattering table: 0.610 Process input model: 243.710 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 266.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 92086 Z= 0.248 Angle : 0.795 13.696 131881 Z= 0.405 Chirality : 0.044 0.502 16096 Planarity : 0.008 0.600 10849 Dihedral : 21.276 179.944 45722 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 0.02 % Allowed : 0.37 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.05 % Twisted Proline : 0.34 % Twisted General : 0.05 % 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: -1.12 (0.10), residues: 6568 helix: -0.25 (0.09), residues: 2775 sheet: -0.48 (0.17), residues: 895 loop : -1.22 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP K 623 HIS 0.011 0.001 HIS u 676 PHE 0.059 0.002 PHE C 236 TYR 0.033 0.002 TYR Z 65 ARG 0.019 0.001 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 673 time to evaluate : 5.782 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: c 35 MET cc_start: 0.3152 (mpp) cc_final: 0.2813 (mmt) REVERT: I 148 LYS cc_start: 0.6983 (tmmt) cc_final: 0.6775 (ttpt) REVERT: K 334 MET cc_start: 0.4403 (mmt) cc_final: 0.4170 (mmt) REVERT: K 509 MET cc_start: -0.2057 (ptt) cc_final: -0.2758 (ptt) REVERT: K 935 MET cc_start: -0.0469 (ppp) cc_final: -0.0877 (ppp) REVERT: A 166 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8314 (mttt) outliers start: 1 outliers final: 0 residues processed: 673 average time/residue: 0.7922 time to fit residues: 921.5250 Evaluate side-chains 515 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 5.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 686 optimal weight: 30.0000 chunk 616 optimal weight: 50.0000 chunk 341 optimal weight: 50.0000 chunk 210 optimal weight: 3.9990 chunk 415 optimal weight: 10.0000 chunk 329 optimal weight: 4.9990 chunk 637 optimal weight: 50.0000 chunk 246 optimal weight: 9.9990 chunk 387 optimal weight: 0.9980 chunk 474 optimal weight: 30.0000 chunk 738 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 ASN B 208 HIS E 157 ASN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS Z 106 GLN X 92 ASN ** t 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 ASN S 19 ASN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 104 GLN O 38 ASN C 136 HIS V 21 ASN ** y 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 92086 Z= 0.421 Angle : 0.718 13.777 131881 Z= 0.363 Chirality : 0.044 0.378 16096 Planarity : 0.006 0.108 10849 Dihedral : 22.489 179.363 32107 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 1.18 % Allowed : 8.52 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.05 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.10), residues: 6568 helix: 0.49 (0.10), residues: 2768 sheet: -0.46 (0.17), residues: 893 loop : -1.15 (0.11), residues: 2907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 623 HIS 0.012 0.001 HIS u 676 PHE 0.049 0.002 PHE J 159 TYR 0.027 0.002 TYR J 35 ARG 0.010 0.001 ARG Y 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 532 time to evaluate : 5.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 77 MET cc_start: 0.5816 (tpp) cc_final: 0.5490 (ttt) REVERT: t 463 LEU cc_start: 0.6635 (pp) cc_final: 0.6390 (tp) REVERT: W 85 ASP cc_start: 0.7212 (t70) cc_final: 0.6858 (t0) REVERT: u 123 MET cc_start: 0.7367 (tpp) cc_final: 0.6926 (tpp) REVERT: A 166 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8425 (mttt) REVERT: V 21 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8274 (t0) REVERT: y 308 MET cc_start: 0.6311 (ppp) cc_final: 0.6056 (ptm) outliers start: 68 outliers final: 49 residues processed: 564 average time/residue: 0.7982 time to fit residues: 779.4939 Evaluate side-chains 551 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 501 time to evaluate : 5.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain b residue 42 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain t residue 352 SER Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain u residue 231 MET Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 740 HIS Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain T residue 116 ASP Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 98 ASN Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain I residue 67 TRP Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain K residue 155 MET Chi-restraints excluded: chain K residue 1002 MET Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain V residue 21 ASN Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 80 SER Chi-restraints excluded: chain y residue 98 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 410 optimal weight: 4.9990 chunk 229 optimal weight: 50.0000 chunk 614 optimal weight: 20.0000 chunk 502 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 739 optimal weight: 4.9990 chunk 799 optimal weight: 0.3980 chunk 658 optimal weight: 7.9990 chunk 733 optimal weight: 20.0000 chunk 252 optimal weight: 2.9990 chunk 593 optimal weight: 30.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 HIS S 72 GLN Q 114 GLN ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN y 271 HIS ** y 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 92086 Z= 0.221 Angle : 0.590 12.503 131881 Z= 0.302 Chirality : 0.038 0.345 16096 Planarity : 0.005 0.112 10849 Dihedral : 22.401 179.784 32107 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 1.41 % Allowed : 11.03 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.10), residues: 6568 helix: 0.86 (0.10), residues: 2786 sheet: -0.41 (0.17), residues: 897 loop : -1.03 (0.11), residues: 2885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP w 213 HIS 0.008 0.001 HIS u 676 PHE 0.030 0.001 PHE y 69 TYR 0.017 0.001 TYR x 238 ARG 0.006 0.000 ARG c 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 533 time to evaluate : 5.941 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 77 MET cc_start: 0.5304 (tpp) cc_final: 0.5018 (ttm) REVERT: t 463 LEU cc_start: 0.6708 (pp) cc_final: 0.6452 (tp) REVERT: W 85 ASP cc_start: 0.7098 (t70) cc_final: 0.6779 (t0) REVERT: O 135 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8445 (tp) REVERT: r 84 MET cc_start: 0.2496 (mmm) cc_final: 0.2199 (mmm) REVERT: A 166 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8406 (mttt) outliers start: 81 outliers final: 56 residues processed: 571 average time/residue: 0.7988 time to fit residues: 789.0333 Evaluate side-chains 567 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 510 time to evaluate : 5.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 42 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain x residue 107 ILE Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 246 SER Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain t residue 363 HIS Chi-restraints excluded: chain t residue 440 GLU Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain u residue 258 VAL Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 729 VAL Chi-restraints excluded: chain u residue 740 HIS Chi-restraints excluded: chain u residue 751 MET Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain T residue 116 ASP Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 125 HIS Chi-restraints excluded: chain Q residue 24 HIS Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 98 ASN Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 67 TRP Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain K residue 155 MET Chi-restraints excluded: chain K residue 1002 MET Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain y residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 730 optimal weight: 10.0000 chunk 556 optimal weight: 3.9990 chunk 383 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 352 optimal weight: 50.0000 chunk 496 optimal weight: 0.9980 chunk 742 optimal weight: 9.9990 chunk 785 optimal weight: 20.0000 chunk 387 optimal weight: 3.9990 chunk 703 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 67 GLN E 188 ASN E 197 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 240 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 92086 Z= 0.287 Angle : 0.619 12.584 131881 Z= 0.316 Chirality : 0.040 0.339 16096 Planarity : 0.005 0.112 10849 Dihedral : 22.353 179.917 32107 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.81 % Rotamer: Outliers : 2.14 % Allowed : 12.54 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.10), residues: 6568 helix: 1.02 (0.10), residues: 2791 sheet: -0.40 (0.17), residues: 888 loop : -0.99 (0.11), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP w 213 HIS 0.011 0.001 HIS P 54 PHE 0.036 0.002 PHE y 69 TYR 0.019 0.001 TYR J 35 ARG 0.009 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 529 time to evaluate : 5.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 169 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9056 (mp) REVERT: t 463 LEU cc_start: 0.6749 (pp) cc_final: 0.6422 (tp) REVERT: W 82 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7961 (mt0) REVERT: W 85 ASP cc_start: 0.7168 (t70) cc_final: 0.6831 (t0) REVERT: u 287 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6915 (ptp-170) REVERT: r 84 MET cc_start: 0.2512 (mmm) cc_final: 0.2189 (mmm) REVERT: V 9 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7916 (m) REVERT: y 409 VAL cc_start: 0.5423 (OUTLIER) cc_final: 0.5066 (m) outliers start: 123 outliers final: 78 residues processed: 606 average time/residue: 0.8148 time to fit residues: 860.3949 Evaluate side-chains 587 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 504 time to evaluate : 5.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 GLN Chi-restraints excluded: chain b residue 42 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain x residue 107 ILE Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 200 THR Chi-restraints excluded: chain x residue 246 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain t residue 355 SER Chi-restraints excluded: chain t residue 363 HIS Chi-restraints excluded: chain t residue 440 GLU Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 82 GLN Chi-restraints excluded: chain u residue 231 MET Chi-restraints excluded: chain u residue 258 VAL Chi-restraints excluded: chain u residue 287 ARG Chi-restraints excluded: chain u residue 289 LEU Chi-restraints excluded: chain u residue 562 VAL Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 729 VAL Chi-restraints excluded: chain u residue 740 HIS Chi-restraints excluded: chain u residue 751 MET Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain T residue 116 ASP Chi-restraints excluded: chain S residue 125 HIS Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 67 TRP Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain K residue 155 MET Chi-restraints excluded: chain K residue 1002 MET Chi-restraints excluded: chain z residue 199 GLU Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain y residue 98 VAL Chi-restraints excluded: chain y residue 409 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 654 optimal weight: 40.0000 chunk 446 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 585 optimal weight: 3.9990 chunk 324 optimal weight: 0.9990 chunk 670 optimal weight: 10.0000 chunk 543 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 401 optimal weight: 10.0000 chunk 705 optimal weight: 9.9990 chunk 198 optimal weight: 50.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 46 HIS ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN J 156 HIS ** y 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 92086 Z= 0.224 Angle : 0.589 12.620 131881 Z= 0.301 Chirality : 0.038 0.366 16096 Planarity : 0.004 0.111 10849 Dihedral : 22.317 179.816 32107 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 2.05 % Allowed : 13.79 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.10), residues: 6568 helix: 1.18 (0.10), residues: 2789 sheet: -0.38 (0.17), residues: 875 loop : -0.93 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP w 213 HIS 0.010 0.001 HIS P 54 PHE 0.033 0.001 PHE y 69 TYR 0.024 0.001 TYR Q 115 ARG 0.008 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 532 time to evaluate : 5.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 50 ILE cc_start: 0.2990 (OUTLIER) cc_final: 0.2788 (mm) REVERT: E 169 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9071 (mp) REVERT: G 91 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.6908 (tt0) REVERT: t 463 LEU cc_start: 0.6717 (pp) cc_final: 0.6405 (tp) REVERT: W 85 ASP cc_start: 0.7155 (t70) cc_final: 0.6809 (t0) REVERT: u 287 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6941 (ptp-170) REVERT: J 159 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8160 (t80) REVERT: r 84 MET cc_start: 0.2466 (mmm) cc_final: 0.2155 (mmm) REVERT: V 9 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7957 (m) outliers start: 118 outliers final: 82 residues processed: 601 average time/residue: 0.8005 time to fit residues: 833.9202 Evaluate side-chains 597 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 509 time to evaluate : 5.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain b residue 42 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain x residue 107 ILE Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 166 THR Chi-restraints excluded: chain x residue 200 THR Chi-restraints excluded: chain x residue 246 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain t residue 355 SER Chi-restraints excluded: chain t residue 363 HIS Chi-restraints excluded: chain t residue 440 GLU Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain u residue 231 MET Chi-restraints excluded: chain u residue 258 VAL Chi-restraints excluded: chain u residue 287 ARG Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 360 ILE Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 729 VAL Chi-restraints excluded: chain u residue 740 HIS Chi-restraints excluded: chain u residue 751 MET Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain T residue 116 ASP Chi-restraints excluded: chain S residue 125 HIS Chi-restraints excluded: chain Q residue 24 HIS Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 67 TRP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain K residue 155 MET Chi-restraints excluded: chain M residue 126 GLU Chi-restraints excluded: chain z residue 199 GLU Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain y residue 68 GLU Chi-restraints excluded: chain y residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 264 optimal weight: 10.0000 chunk 707 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 461 optimal weight: 0.5980 chunk 193 optimal weight: 7.9990 chunk 786 optimal weight: 4.9990 chunk 652 optimal weight: 40.0000 chunk 364 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 chunk 412 optimal weight: 0.8980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 92086 Z= 0.281 Angle : 0.620 12.631 131881 Z= 0.315 Chirality : 0.040 0.362 16096 Planarity : 0.005 0.112 10849 Dihedral : 22.296 179.914 32107 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.86 % Rotamer: Outliers : 2.33 % Allowed : 14.70 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.10), residues: 6568 helix: 1.25 (0.10), residues: 2794 sheet: -0.39 (0.17), residues: 896 loop : -0.94 (0.11), residues: 2878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP w 213 HIS 0.008 0.001 HIS P 54 PHE 0.039 0.002 PHE y 69 TYR 0.028 0.001 TYR R 53 ARG 0.008 0.000 ARG b 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 520 time to evaluate : 5.761 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: c 35 MET cc_start: 0.3587 (mpp) cc_final: 0.3350 (mpp) REVERT: E 169 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9073 (mp) REVERT: G 72 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7068 (ptp-110) REVERT: G 91 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: W 82 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7989 (mt0) REVERT: W 85 ASP cc_start: 0.7187 (t70) cc_final: 0.6830 (t0) REVERT: W 125 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8753 (tp) REVERT: u 287 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6889 (ptp90) REVERT: P 89 MET cc_start: 0.6294 (mmt) cc_final: 0.6039 (mmt) REVERT: J 159 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8222 (t80) REVERT: I 181 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8116 (mm110) REVERT: r 84 MET cc_start: 0.2277 (mmm) cc_final: 0.1993 (mmm) REVERT: C 124 PHE cc_start: 0.5063 (m-10) cc_final: 0.4800 (m-10) REVERT: V 9 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7957 (m) outliers start: 134 outliers final: 94 residues processed: 609 average time/residue: 0.8044 time to fit residues: 848.2310 Evaluate side-chains 613 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 510 time to evaluate : 7.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 42 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain x residue 107 ILE Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 166 THR Chi-restraints excluded: chain x residue 200 THR Chi-restraints excluded: chain x residue 246 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain t residue 355 SER Chi-restraints excluded: chain t residue 363 HIS Chi-restraints excluded: chain t residue 440 GLU Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 82 GLN Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 231 MET Chi-restraints excluded: chain u residue 258 VAL Chi-restraints excluded: chain u residue 287 ARG Chi-restraints excluded: chain u residue 289 LEU Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 360 ILE Chi-restraints excluded: chain u residue 579 LEU Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 729 VAL Chi-restraints excluded: chain u residue 751 MET Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain T residue 116 ASP Chi-restraints excluded: chain S residue 125 HIS Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 70 LYS Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 67 TRP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 154 LYS Chi-restraints excluded: chain I residue 181 GLN Chi-restraints excluded: chain K residue 155 MET Chi-restraints excluded: chain M residue 126 GLU Chi-restraints excluded: chain z residue 199 GLU Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain y residue 98 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 758 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 448 optimal weight: 0.9990 chunk 574 optimal weight: 4.9990 chunk 445 optimal weight: 2.9990 chunk 662 optimal weight: 30.0000 chunk 439 optimal weight: 10.0000 chunk 783 optimal weight: 10.0000 chunk 490 optimal weight: 40.0000 chunk 477 optimal weight: 7.9990 chunk 361 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 92086 Z= 0.387 Angle : 0.691 14.056 131881 Z= 0.348 Chirality : 0.043 0.363 16096 Planarity : 0.005 0.112 10849 Dihedral : 22.350 179.423 32107 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 2.71 % Allowed : 14.92 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.10), residues: 6568 helix: 1.20 (0.10), residues: 2786 sheet: -0.55 (0.17), residues: 894 loop : -1.01 (0.11), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP w 213 HIS 0.008 0.001 HIS u 676 PHE 0.036 0.002 PHE J 147 TYR 0.033 0.002 TYR R 53 ARG 0.010 0.001 ARG c 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 520 time to evaluate : 5.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 169 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9080 (mp) REVERT: G 72 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7181 (ptp-110) REVERT: G 91 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: w 27 ASN cc_start: 0.5743 (m-40) cc_final: 0.5535 (m-40) REVERT: W 82 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7967 (mt0) REVERT: W 85 ASP cc_start: 0.7231 (t70) cc_final: 0.6872 (t0) REVERT: W 125 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8735 (tp) REVERT: u 287 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6924 (ptp90) REVERT: J 159 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8306 (t80) REVERT: I 181 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: r 84 MET cc_start: 0.2432 (mmm) cc_final: 0.2143 (mmm) REVERT: K 935 MET cc_start: -0.0915 (ppp) cc_final: -0.1194 (ppp) REVERT: A 165 ASN cc_start: 0.7274 (p0) cc_final: 0.7033 (p0) REVERT: V 9 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7981 (m) outliers start: 156 outliers final: 112 residues processed: 630 average time/residue: 0.8054 time to fit residues: 878.3683 Evaluate side-chains 627 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 506 time to evaluate : 5.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain b residue 42 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 166 THR Chi-restraints excluded: chain x residue 200 THR Chi-restraints excluded: chain x residue 246 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 87 ASN Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 271 HIS Chi-restraints excluded: chain t residue 355 SER Chi-restraints excluded: chain t residue 363 HIS Chi-restraints excluded: chain t residue 440 GLU Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 82 GLN Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain u residue 168 SER Chi-restraints excluded: chain u residue 231 MET Chi-restraints excluded: chain u residue 258 VAL Chi-restraints excluded: chain u residue 287 ARG Chi-restraints excluded: chain u residue 289 LEU Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 360 ILE Chi-restraints excluded: chain u residue 579 LEU Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 729 VAL Chi-restraints excluded: chain u residue 751 MET Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain T residue 116 ASP Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 125 HIS Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 70 LYS Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 67 TRP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 154 LYS Chi-restraints excluded: chain I residue 181 GLN Chi-restraints excluded: chain q residue 193 ASN Chi-restraints excluded: chain K residue 542 MET Chi-restraints excluded: chain K residue 623 TRP Chi-restraints excluded: chain M residue 126 GLU Chi-restraints excluded: chain z residue 199 GLU Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain V residue 80 SER Chi-restraints excluded: chain y residue 98 VAL Chi-restraints excluded: chain y residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 484 optimal weight: 30.0000 chunk 312 optimal weight: 20.0000 chunk 468 optimal weight: 0.0870 chunk 236 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 498 optimal weight: 7.9990 chunk 533 optimal weight: 0.0000 chunk 387 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 615 optimal weight: 30.0000 overall best weight: 3.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN E 197 ASN ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 131 HIS ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** y 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 92086 Z= 0.263 Angle : 0.624 12.645 131881 Z= 0.317 Chirality : 0.039 0.327 16096 Planarity : 0.005 0.112 10849 Dihedral : 22.326 179.965 32107 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.86 % Rotamer: Outliers : 2.37 % Allowed : 15.59 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.10), residues: 6568 helix: 1.25 (0.10), residues: 2798 sheet: -0.55 (0.17), residues: 888 loop : -0.97 (0.11), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP w 213 HIS 0.007 0.001 HIS F 101 PHE 0.034 0.001 PHE y 69 TYR 0.018 0.001 TYR R 53 ARG 0.008 0.000 ARG T 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 516 time to evaluate : 7.371 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 169 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9075 (mp) REVERT: G 72 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7178 (ptp-110) REVERT: G 91 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.6913 (tt0) REVERT: w 27 ASN cc_start: 0.5821 (m-40) cc_final: 0.5614 (m-40) REVERT: W 82 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: W 85 ASP cc_start: 0.7207 (t70) cc_final: 0.6873 (t0) REVERT: W 125 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8736 (tp) REVERT: u 287 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6904 (ptp90) REVERT: J 159 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8250 (t80) REVERT: I 181 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.8071 (mm110) REVERT: r 84 MET cc_start: 0.2664 (mmm) cc_final: 0.2332 (mmm) REVERT: K 935 MET cc_start: -0.0937 (ppp) cc_final: -0.1194 (ppp) REVERT: A 41 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6418 (tpt-90) REVERT: A 47 TYR cc_start: 0.7461 (m-80) cc_final: 0.7021 (m-80) REVERT: A 165 ASN cc_start: 0.7213 (p0) cc_final: 0.6975 (p0) REVERT: V 9 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7986 (m) outliers start: 136 outliers final: 104 residues processed: 608 average time/residue: 0.8084 time to fit residues: 854.6356 Evaluate side-chains 623 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 509 time to evaluate : 5.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 42 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 166 THR Chi-restraints excluded: chain x residue 200 THR Chi-restraints excluded: chain x residue 246 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 87 ASN Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain t residue 355 SER Chi-restraints excluded: chain t residue 363 HIS Chi-restraints excluded: chain t residue 440 GLU Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 82 GLN Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 168 SER Chi-restraints excluded: chain u residue 231 MET Chi-restraints excluded: chain u residue 258 VAL Chi-restraints excluded: chain u residue 287 ARG Chi-restraints excluded: chain u residue 289 LEU Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 344 LEU Chi-restraints excluded: chain u residue 360 ILE Chi-restraints excluded: chain u residue 579 LEU Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 740 HIS Chi-restraints excluded: chain u residue 751 MET Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 70 LYS Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain L residue 15 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 49 THR Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 67 TRP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 181 GLN Chi-restraints excluded: chain K residue 155 MET Chi-restraints excluded: chain K residue 542 MET Chi-restraints excluded: chain K residue 623 TRP Chi-restraints excluded: chain K residue 1002 MET Chi-restraints excluded: chain M residue 126 GLU Chi-restraints excluded: chain z residue 199 GLU Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain V residue 80 SER Chi-restraints excluded: chain y residue 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 712 optimal weight: 50.0000 chunk 750 optimal weight: 7.9990 chunk 684 optimal weight: 8.9990 chunk 730 optimal weight: 0.0370 chunk 439 optimal weight: 4.9990 chunk 318 optimal weight: 0.8980 chunk 573 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 659 optimal weight: 50.0000 chunk 690 optimal weight: 20.0000 chunk 727 optimal weight: 0.0070 overall best weight: 0.9078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS w 22 GLN ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 290 HIS ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN y 318 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 92086 Z= 0.145 Angle : 0.569 12.660 131881 Z= 0.289 Chirality : 0.036 0.279 16096 Planarity : 0.004 0.111 10849 Dihedral : 22.247 179.907 32107 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.21 % Rotamer: Outliers : 1.55 % Allowed : 16.59 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 6568 helix: 1.36 (0.10), residues: 2798 sheet: -0.46 (0.17), residues: 873 loop : -0.82 (0.11), residues: 2897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP K 390 HIS 0.007 0.001 HIS F 101 PHE 0.030 0.001 PHE w 287 TYR 0.020 0.001 TYR R 53 ARG 0.009 0.000 ARG R 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 539 time to evaluate : 5.913 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: b 45 THR cc_start: 0.7425 (p) cc_final: 0.6992 (p) REVERT: G 91 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.6750 (tt0) REVERT: W 82 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: W 85 ASP cc_start: 0.7159 (t70) cc_final: 0.6838 (t0) REVERT: W 125 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8759 (tp) REVERT: J 159 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8159 (t80) REVERT: r 84 MET cc_start: 0.2611 (mmm) cc_final: 0.2296 (mmm) REVERT: K 935 MET cc_start: -0.1069 (ppp) cc_final: -0.1326 (ppp) REVERT: A 41 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6020 (tpt-90) REVERT: A 47 TYR cc_start: 0.7451 (m-80) cc_final: 0.6894 (m-80) REVERT: A 165 ASN cc_start: 0.7094 (p0) cc_final: 0.6835 (p0) REVERT: V 9 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7889 (m) outliers start: 89 outliers final: 66 residues processed: 596 average time/residue: 0.8416 time to fit residues: 868.5393 Evaluate side-chains 591 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 519 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 200 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain w residue 271 HIS Chi-restraints excluded: chain t residue 363 HIS Chi-restraints excluded: chain t residue 440 GLU Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 82 GLN Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 258 VAL Chi-restraints excluded: chain u residue 289 LEU Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 360 ILE Chi-restraints excluded: chain u residue 579 LEU Chi-restraints excluded: chain u residue 740 HIS Chi-restraints excluded: chain u residue 751 MET Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 109 MET Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 67 TRP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain q residue 193 ASN Chi-restraints excluded: chain K residue 155 MET Chi-restraints excluded: chain K residue 542 MET Chi-restraints excluded: chain K residue 623 TRP Chi-restraints excluded: chain K residue 1002 MET Chi-restraints excluded: chain M residue 126 GLU Chi-restraints excluded: chain z residue 199 GLU Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain y residue 98 VAL Chi-restraints excluded: chain y residue 318 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 479 optimal weight: 10.0000 chunk 772 optimal weight: 2.9990 chunk 471 optimal weight: 0.0470 chunk 366 optimal weight: 8.9990 chunk 536 optimal weight: 0.2980 chunk 809 optimal weight: 4.9990 chunk 745 optimal weight: 8.9990 chunk 644 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 498 optimal weight: 20.0000 chunk 395 optimal weight: 4.9990 overall best weight: 2.6684 ------------------------------------------------------------------------------- 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 208 HIS E 197 ASN H 68 GLN ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 131 HIS ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN y 290 ASN y 318 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 92086 Z= 0.221 Angle : 0.599 12.639 131881 Z= 0.303 Chirality : 0.038 0.309 16096 Planarity : 0.004 0.125 10849 Dihedral : 22.197 179.981 32107 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 1.53 % Allowed : 16.87 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.11), residues: 6568 helix: 1.38 (0.10), residues: 2806 sheet: -0.49 (0.17), residues: 871 loop : -0.82 (0.11), residues: 2891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP K 390 HIS 0.009 0.001 HIS F 101 PHE 0.034 0.001 PHE y 69 TYR 0.017 0.001 TYR R 53 ARG 0.010 0.000 ARG H 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13136 Ramachandran restraints generated. 6568 Oldfield, 0 Emsley, 6568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 516 time to evaluate : 5.879 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 91 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.6852 (tt0) REVERT: W 82 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: W 85 ASP cc_start: 0.7188 (t70) cc_final: 0.6853 (t0) REVERT: W 125 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8745 (tp) REVERT: J 159 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8049 (t80) REVERT: r 84 MET cc_start: 0.2607 (mmm) cc_final: 0.2287 (mmm) REVERT: K 935 MET cc_start: -0.1078 (ppp) cc_final: -0.1332 (ppp) REVERT: A 41 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6221 (tpt-90) REVERT: A 47 TYR cc_start: 0.7475 (m-80) cc_final: 0.7005 (m-80) REVERT: A 165 ASN cc_start: 0.7157 (p0) cc_final: 0.6906 (p0) REVERT: V 9 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7976 (m) outliers start: 88 outliers final: 70 residues processed: 576 average time/residue: 0.8347 time to fit residues: 838.5008 Evaluate side-chains 585 residues out of total 5786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 509 time to evaluate : 5.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 200 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 271 HIS Chi-restraints excluded: chain t residue 440 GLU Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain t residue 469 ASN Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 82 GLN Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain u residue 131 HIS Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 258 VAL Chi-restraints excluded: chain u residue 289 LEU Chi-restraints excluded: chain u residue 296 ASP Chi-restraints excluded: chain u residue 360 ILE Chi-restraints excluded: chain u residue 740 HIS Chi-restraints excluded: chain u residue 751 MET Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 70 LYS Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 67 TRP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain q residue 193 ASN Chi-restraints excluded: chain K residue 155 MET Chi-restraints excluded: chain K residue 542 MET Chi-restraints excluded: chain K residue 623 TRP Chi-restraints excluded: chain K residue 1002 MET Chi-restraints excluded: chain M residue 126 GLU Chi-restraints excluded: chain z residue 199 GLU Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain y residue 98 VAL Chi-restraints excluded: chain y residue 318 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 512 optimal weight: 1.9990 chunk 687 optimal weight: 30.0000 chunk 197 optimal weight: 4.9990 chunk 594 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 645 optimal weight: 20.0000 chunk 270 optimal weight: 0.8980 chunk 663 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 118 optimal weight: 50.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 208 HIS E 197 ASN H 76 GLN ** w 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 131 HIS ** P 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 318 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.142773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.127720 restraints weight = 184761.871| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 0.71 r_work: 0.3860 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 92086 Z= 0.312 Angle : 0.650 14.735 131881 Z= 0.328 Chirality : 0.040 0.335 16096 Planarity : 0.005 0.112 10849 Dihedral : 22.228 179.921 32107 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.87 % Rotamer: Outliers : 1.76 % Allowed : 16.70 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.10), residues: 6568 helix: 1.35 (0.10), residues: 2797 sheet: -0.59 (0.17), residues: 885 loop : -0.89 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.002 TRP w 213 HIS 0.010 0.001 HIS F 101 PHE 0.037 0.002 PHE y 69 TYR 0.018 0.001 TYR B 133 ARG 0.010 0.000 ARG y 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15867.07 seconds wall clock time: 283 minutes 57.04 seconds (17037.04 seconds total)