Starting phenix.real_space_refine on Sat Jun 28 17:28:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xo0_38521/06_2025/8xo0_38521_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xo0_38521/06_2025/8xo0_38521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xo0_38521/06_2025/8xo0_38521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xo0_38521/06_2025/8xo0_38521.map" model { file = "/net/cci-nas-00/data/ceres_data/8xo0_38521/06_2025/8xo0_38521_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xo0_38521/06_2025/8xo0_38521_neut.cif" } resolution = 4.2 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= 0.005 sd= 0.064 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 Fe 28 7.16 5 P 9 5.49 5 S 244 5.16 5 C 21573 2.51 5 N 5754 2.21 5 O 6121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33729 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 737 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3088 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 21, 'TRANS': 363} Chain: "E" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1635 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 21, 'TRANS': 188} Chain: "F" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3273 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 21, 'TRANS': 402} Chain: "G" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5287 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 31, 'TRANS': 655} Chain: "H" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2531 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 22, 'TRANS': 294} Chain breaks: 1 Chain: "I" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1389 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 1 Chain: "P" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2720 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 19, 'TRANS': 319} Chain: "Q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 957 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 587 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain breaks: 1 Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1164 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 11, 'TRANS': 67} Chain: "q" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1020 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 9, 'TRANS': 112} Chain breaks: 1 Chain: "r" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 418 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain breaks: 1 Chain: "s" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 989 SG CYS B 99 80.889 59.228 105.802 1.00 29.52 S ATOM 1492 SG CYS B 164 78.543 54.714 110.570 1.00 28.96 S ATOM 1722 SG CYS B 194 83.680 54.403 109.755 1.00 29.28 S ATOM 995 SG CYS B 100 79.931 54.511 104.262 1.00 30.11 S ATOM 7502 SG CYS E 134 141.102 48.678 151.643 1.00 56.01 S ATOM 7536 SG CYS E 139 144.002 49.725 151.245 1.00 56.50 S ATOM 7843 SG CYS E 179 142.610 54.056 154.665 1.00 57.95 S ATOM 10997 SG CYS F 379 120.370 53.100 154.046 1.00 43.09 S ATOM 11016 SG CYS F 382 118.399 57.331 150.402 1.00 40.29 S ATOM 11036 SG CYS F 385 122.723 55.829 148.841 1.00 39.95 S ATOM 11358 SG CYS F 425 122.805 58.421 154.585 1.00 45.60 S ATOM 12406 SG CYS G 131 101.881 46.251 137.921 1.00 31.31 S ATOM 12385 SG CYS G 128 103.976 49.944 133.239 1.00 30.26 S ATOM 12446 SG CYS G 137 101.740 52.188 139.237 1.00 33.13 S ATOM 13131 SG CYS G 226 103.475 46.366 146.497 1.00 34.31 S ATOM 12802 SG CYS G 182 106.608 44.700 152.259 1.00 36.31 S ATOM 12778 SG CYS G 179 106.141 50.248 149.619 1.00 35.62 S ATOM 12755 SG CYS G 176 109.433 45.834 147.204 1.00 34.05 S ATOM 11892 SG CYS G 64 107.690 56.798 152.581 1.00 35.53 S ATOM 11978 SG CYS G 75 108.403 58.001 149.770 1.00 36.47 S ATOM 12003 SG CYS G 78 107.768 62.548 151.664 1.00 36.76 S ATOM 12104 SG CYS G 92 107.315 60.946 155.059 1.00 39.04 S ATOM 20116 SG CYS I 123 86.716 49.549 119.594 1.00 27.30 S ATOM 20342 SG CYS I 152 87.068 48.135 113.232 1.00 27.39 S ATOM 20389 SG CYS I 158 92.890 48.237 115.985 1.00 26.60 S ATOM 20368 SG CYS I 155 90.363 53.149 115.730 1.00 27.04 S ATOM 20065 SG CYS I 116 97.259 45.250 126.419 1.00 29.24 S ATOM 20088 SG CYS I 119 93.168 44.923 122.740 1.00 28.85 S ATOM 20046 SG CYS I 113 95.952 40.093 123.247 1.00 28.61 S ATOM 20418 SG CYS I 162 98.972 44.572 121.058 1.00 28.07 S Time building chain proxies: 20.21, per 1000 atoms: 0.60 Number of scatterers: 33729 At special positions: 0 Unit cell: (169.32, 126.99, 202.52, 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) Fe 28 26.01 S 244 16.00 P 9 15.00 O 6121 8.00 N 5754 7.00 C 21573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.04 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 9.03 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 164 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb=" SF4 F 502 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb=" SF4 I 302 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 302 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 303 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 162 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 113 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 119 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 116 " Number of angles added : 81 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7822 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 35 sheets defined 50.4% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 83 through 108 Processing helix chain 'B' and resid 70 through 89 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.547A pdb=" N ALA B 128 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.592A pdb=" N TYR B 171 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 215 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'C' and resid 50 through 68 removed outlier: 3.604A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.319A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.115A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.967A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.297A pdb=" N LEU D 130 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.772A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.861A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.706A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 3.690A pdb=" N ASP D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.669A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 439 removed outlier: 3.528A pdb=" N LEU D 435 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 453 Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.617A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.525A pdb=" N VAL E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 143 through 156 Processing helix chain 'E' and resid 196 through 209 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 84 removed outlier: 3.602A pdb=" N GLY F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Proline residue: F 73 - end of helix Processing helix chain 'F' and resid 94 through 102 removed outlier: 4.233A pdb=" N MET F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.649A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.847A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.711A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN F 168 " --> pdb=" O ASN F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.831A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 258 removed outlier: 3.601A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix Processing helix chain 'F' and resid 258 through 265 removed outlier: 3.919A pdb=" N PHE F 262 " --> pdb=" O GLY F 258 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 Processing helix chain 'F' and resid 328 through 335 removed outlier: 4.062A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR F 334 " --> pdb=" O SER F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.546A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.660A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.646A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.349A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.517A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.774A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.713A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 147 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.930A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.819A pdb=" N ASP G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 Processing helix chain 'G' and resid 295 through 297 No H-bonds generated for 'chain 'G' and resid 295 through 297' Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'G' and resid 390 through 395 removed outlier: 4.190A pdb=" N GLU G 395 " --> pdb=" O ILE G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.024A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 458 removed outlier: 4.287A pdb=" N GLN G 453 " --> pdb=" O PRO G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 469 removed outlier: 4.114A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.635A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.523A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.641A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 10 through 32 removed outlier: 3.750A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.574A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 86 Proline residue: H 75 - end of helix removed outlier: 3.625A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 124 removed outlier: 4.465A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN H 124 " --> pdb=" O GLY H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.553A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.736A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 203 removed outlier: 3.908A pdb=" N GLY H 203 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 213 removed outlier: 3.547A pdb=" N VAL H 213 " --> pdb=" O GLY H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 277 removed outlier: 3.932A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 63 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.618A pdb=" N GLY I 69 " --> pdb=" O GLU I 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 123 Processing helix chain 'I' and resid 156 through 162 Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.865A pdb=" N LEU I 183 " --> pdb=" O THR I 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 179 through 183' Processing helix chain 'I' and resid 186 through 209 removed outlier: 5.146A pdb=" N ALA I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.783A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 96 removed outlier: 4.899A pdb=" N HIS P 93 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU P 94 " --> pdb=" O ASP P 90 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 122 removed outlier: 4.104A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N HIS P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'P' and resid 146 through 160 removed outlier: 3.627A pdb=" N ALA P 153 " --> pdb=" O PRO P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 195 removed outlier: 3.624A pdb=" N SER P 193 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 219 removed outlier: 4.163A pdb=" N PHE P 217 " --> pdb=" O PHE P 213 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA P 218 " --> pdb=" O LEU P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 223 Processing helix chain 'P' and resid 229 through 233 Processing helix chain 'P' and resid 242 through 255 Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.622A pdb=" N TRP P 300 " --> pdb=" O PHE P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 323 Processing helix chain 'P' and resid 335 through 339 Processing helix chain 'P' and resid 344 through 354 removed outlier: 4.034A pdb=" N LYS P 348 " --> pdb=" O PRO P 344 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU P 351 " --> pdb=" O LEU P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 357 No H-bonds generated for 'chain 'P' and resid 355 through 357' Processing helix chain 'P' and resid 360 through 364 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.414A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 130 through 142 Processing helix chain 'Q' and resid 159 through 164 removed outlier: 4.200A pdb=" N ASN Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE Q 164 " --> pdb=" O TYR Q 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 159 through 164' Processing helix chain 'R' and resid 44 through 49 Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'S' and resid 30 through 48 removed outlier: 6.446A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 removed outlier: 3.811A pdb=" N TYR T 90 " --> pdb=" O VAL T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 127 Processing helix chain 'T' and resid 133 through 138 removed outlier: 3.625A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.678A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.584A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 removed outlier: 3.928A pdb=" N ASN W 73 " --> pdb=" O MET W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 98 Processing helix chain 'W' and resid 102 through 108 Processing helix chain 'W' and resid 109 through 111 No H-bonds generated for 'chain 'W' and resid 109 through 111' Processing helix chain 'W' and resid 120 through 128 Processing helix chain 'X' and resid 10 through 14 removed outlier: 3.527A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 36 removed outlier: 4.623A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 50 Processing helix chain 'X' and resid 52 through 77 removed outlier: 4.273A pdb=" N CYS X 56 " --> pdb=" O ASP X 52 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS X 58 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLU X 59 " --> pdb=" O ARG X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.945A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 Processing helix chain 'X' and resid 140 through 144 removed outlier: 4.148A pdb=" N SER X 144 " --> pdb=" O PRO X 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 98 Proline residue: Z 73 - end of helix removed outlier: 3.906A pdb=" N MET Z 98 " --> pdb=" O GLU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 4 through 31 removed outlier: 4.499A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 4.634A pdb=" N LYS a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR a 30 " --> pdb=" O ILE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 55 Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 18 through 32 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.760A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.602A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 Processing helix chain 'q' and resid 78 through 82 removed outlier: 3.537A pdb=" N VAL q 82 " --> pdb=" O GLY q 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 91 removed outlier: 4.127A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 7 through 17 Processing helix chain 's' and resid 43 through 53 Processing helix chain 's' and resid 54 through 56 No H-bonds generated for 'chain 's' and resid 54 through 56' Processing sheet with id=AA1, first strand: chain 'B' and resid 131 through 134 removed outlier: 6.066A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 72 through 74 removed outlier: 3.522A pdb=" N GLN C 74 " --> pdb=" O CYS C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 117 removed outlier: 6.045A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.149A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.563A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.616A pdb=" N MET D 80 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL D 98 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N CYS D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU D 100 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS D 442 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.310A pdb=" N VAL D 318 " --> pdb=" O LYS I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 397 through 401 Processing sheet with id=AB1, first strand: chain 'E' and resid 171 through 173 removed outlier: 3.702A pdb=" N CYS E 134 " --> pdb=" O MET E 184 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N MET E 184 " --> pdb=" O CYS E 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 194 through 199 removed outlier: 7.393A pdb=" N ARG F 152 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE F 196 " --> pdb=" O ARG F 152 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LYS F 111 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N TYR F 155 " --> pdb=" O LYS F 111 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR F 157 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 286 through 287 removed outlier: 6.348A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL F 356 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 294 through 295 removed outlier: 4.075A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 32 through 34 removed outlier: 3.730A pdb=" N VAL G 34 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 89 through 90 Processing sheet with id=AB7, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB8, first strand: chain 'G' and resid 246 through 251 removed outlier: 8.153A pdb=" N ASN G 260 " --> pdb=" O PRO G 275 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL G 262 " --> pdb=" O ILE G 273 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE G 273 " --> pdb=" O VAL G 262 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER G 264 " --> pdb=" O MET G 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 299 through 301 removed outlier: 5.944A pdb=" N HIS q 135 " --> pdb=" O ARG G 299 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 307 through 308 Processing sheet with id=AC2, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.093A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA G 339 " --> pdb=" O PHE G 546 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU G 548 " --> pdb=" O ALA G 339 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE G 341 " --> pdb=" O LEU G 548 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.203A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC6, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.407A pdb=" N GLU I 133 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.226A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL P 126 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL P 167 " --> pdb=" O VAL P 126 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN P 128 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE P 200 " --> pdb=" O PHE P 263 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 205 through 207 removed outlier: 6.216A pdb=" N ASP P 205 " --> pdb=" O VAL P 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'P' and resid 226 through 227 removed outlier: 5.710A pdb=" N VAL P 226 " --> pdb=" O TYR P 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'P' and resid 236 through 237 Processing sheet with id=AD2, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AD3, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD4, first strand: chain 'R' and resid 76 through 79 removed outlier: 4.032A pdb=" N VAL R 91 " --> pdb=" O CYS R 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.508A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 53 through 56 removed outlier: 3.671A pdb=" N GLN S 73 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 130 through 131 Processing sheet with id=AD8, first strand: chain 'q' and resid 37 through 42 removed outlier: 6.238A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN q 46 " --> pdb=" O ASP q 42 " (cutoff:3.500A) 1439 hydrogen bonds defined for protein. 4155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.53 Time building geometry restraints manager: 10.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.35: 10941 1.35 - 1.57: 23115 1.57 - 1.79: 199 1.79 - 2.01: 207 2.01 - 2.24: 80 Bond restraints: 34542 Sorted by residual: bond pdb=" N PRO X 53 " pdb=" CD PRO X 53 " ideal model delta sigma weight residual 1.473 1.204 0.269 1.40e-02 5.10e+03 3.68e+02 bond pdb=" C ALA E 227 " pdb=" O ALA E 227 " ideal model delta sigma weight residual 1.236 1.419 -0.183 1.16e-02 7.43e+03 2.50e+02 bond pdb=" N PRO R 89 " pdb=" CD PRO R 89 " ideal model delta sigma weight residual 1.473 1.260 0.213 1.40e-02 5.10e+03 2.31e+02 bond pdb=" N PRO q 139 " pdb=" CD PRO q 139 " ideal model delta sigma weight residual 1.473 1.282 0.191 1.40e-02 5.10e+03 1.85e+02 bond pdb=" N PRO P 371 " pdb=" CD PRO P 371 " ideal model delta sigma weight residual 1.473 1.653 -0.180 1.40e-02 5.10e+03 1.65e+02 ... (remaining 34537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 45562 5.06 - 10.12: 979 10.12 - 15.17: 187 15.17 - 20.23: 90 20.23 - 25.29: 4 Bond angle restraints: 46822 Sorted by residual: angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" CB VAL D 142 " ideal model delta sigma weight residual 110.65 132.46 -21.81 1.13e+00 7.83e-01 3.73e+02 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 110.42 92.51 17.91 9.40e-01 1.13e+00 3.63e+02 angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.39 89.10 25.29 1.45e+00 4.76e-01 3.04e+02 angle pdb=" N CYS F 332 " pdb=" CA CYS F 332 " pdb=" C CYS F 332 " ideal model delta sigma weight residual 111.02 130.01 -18.99 1.22e+00 6.72e-01 2.42e+02 angle pdb=" N PRO X 53 " pdb=" CA PRO X 53 " pdb=" CB PRO X 53 " ideal model delta sigma weight residual 103.46 89.89 13.57 9.30e-01 1.16e+00 2.13e+02 ... (remaining 46817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 20240 28.38 - 56.75: 529 56.75 - 85.13: 57 85.13 - 113.51: 5 113.51 - 141.88: 1 Dihedral angle restraints: 20832 sinusoidal: 8699 harmonic: 12133 Sorted by residual: dihedral pdb=" N GLU r 91 " pdb=" C GLU r 91 " pdb=" CA GLU r 91 " pdb=" CB GLU r 91 " ideal model delta harmonic sigma weight residual 122.80 167.18 -44.38 0 2.50e+00 1.60e-01 3.15e+02 dihedral pdb=" C GLU r 91 " pdb=" N GLU r 91 " pdb=" CA GLU r 91 " pdb=" CB GLU r 91 " ideal model delta harmonic sigma weight residual -122.60 -162.78 40.18 0 2.50e+00 1.60e-01 2.58e+02 dihedral pdb=" N PRO X 53 " pdb=" C PRO X 53 " pdb=" CA PRO X 53 " pdb=" CB PRO X 53 " ideal model delta harmonic sigma weight residual 115.10 92.24 22.86 0 2.50e+00 1.60e-01 8.36e+01 ... (remaining 20829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 5054 0.349 - 0.697: 56 0.697 - 1.046: 24 1.046 - 1.395: 0 1.395 - 1.743: 1 Chirality restraints: 5135 Sorted by residual: chirality pdb=" CA GLU r 91 " pdb=" N GLU r 91 " pdb=" C GLU r 91 " pdb=" CB GLU r 91 " both_signs ideal model delta sigma weight residual False 2.51 0.77 1.74 2.00e-01 2.50e+01 7.60e+01 chirality pdb="FE2 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S3 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False 10.55 9.64 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb="FE4 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S3 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.91 2.00e-01 2.50e+01 2.05e+01 ... (remaining 5132 not shown) Planarity restraints: 5952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 41 " 0.089 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO H 42 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO H 42 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO H 42 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 224 " 0.025 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C GLU C 224 " -0.087 2.00e-02 2.50e+03 pdb=" O GLU C 224 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU C 225 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 223 " 0.020 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C HIS D 223 " -0.073 2.00e-02 2.50e+03 pdb=" O HIS D 223 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA D 224 " 0.025 2.00e-02 2.50e+03 ... (remaining 5949 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 46 2.34 - 2.98: 21025 2.98 - 3.62: 52554 3.62 - 4.26: 84055 4.26 - 4.90: 136421 Nonbonded interactions: 294101 Sorted by model distance: nonbonded pdb=" O ASN F 270 " pdb=" OD1 ASN F 270 " model vdw 1.702 3.040 nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.755 3.040 nonbonded pdb=" O ASP q 76 " pdb=" OD1 ASP q 76 " model vdw 1.904 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASN P 376 " pdb=" N TYR P 377 " model vdw 1.979 3.120 ... (remaining 294096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.490 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: 0.020 Extract box with map and model: 1.360 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 80.940 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 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 : 0.020 1.140 34578 Z= 0.993 Angle : 2.159 41.383 46909 Z= 1.459 Chirality : 0.126 1.743 5135 Planarity : 0.007 0.134 5952 Dihedral : 12.568 141.882 13001 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 41.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 0.28 % Allowed : 6.98 % Favored : 92.75 % Cbeta Deviations : 1.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.12), residues: 4127 helix: -0.70 (0.11), residues: 1799 sheet: -1.09 (0.30), residues: 313 loop : -2.07 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 285 HIS 0.012 0.002 HIS C 159 PHE 0.050 0.002 PHE a 3 TYR 0.045 0.002 TYR B 112 ARG 0.008 0.001 ARG D 333 Details of bonding type rmsd hydrogen bonds : bond 0.23930 ( 1439) hydrogen bonds : angle 8.88220 ( 4155) metal coordination : bond 0.48059 ( 33) metal coordination : angle 16.44467 ( 81) SS BOND : bond 0.00806 ( 3) SS BOND : angle 2.22935 ( 6) covalent geometry : bond 0.01391 (34542) covalent geometry : angle 2.04924 (46822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1477 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1467 time to evaluate : 3.470 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8157 (m-40) cc_final: 0.7329 (t0) REVERT: A 92 PHE cc_start: 0.5106 (m-10) cc_final: 0.4724 (m-10) REVERT: B 106 HIS cc_start: 0.7525 (m-70) cc_final: 0.7307 (m90) REVERT: B 145 LEU cc_start: 0.8512 (tp) cc_final: 0.8301 (tp) REVERT: B 170 TYR cc_start: 0.8066 (t80) cc_final: 0.7621 (t80) REVERT: B 175 TYR cc_start: 0.8031 (p90) cc_final: 0.7815 (p90) REVERT: B 202 LEU cc_start: 0.8438 (tm) cc_final: 0.7735 (tm) REVERT: B 208 LEU cc_start: 0.8973 (tp) cc_final: 0.8771 (tt) REVERT: C 93 ILE cc_start: 0.8059 (mm) cc_final: 0.7342 (mm) REVERT: C 141 ARG cc_start: 0.7639 (ttm170) cc_final: 0.7373 (ttm110) REVERT: C 171 ASP cc_start: 0.7672 (t0) cc_final: 0.7408 (t0) REVERT: D 116 LEU cc_start: 0.8437 (tp) cc_final: 0.8151 (mt) REVERT: D 135 TYR cc_start: 0.8130 (m-80) cc_final: 0.7193 (m-10) REVERT: D 189 THR cc_start: 0.7883 (m) cc_final: 0.7077 (m) REVERT: D 222 MET cc_start: 0.7446 (ptm) cc_final: 0.7231 (ptt) REVERT: D 261 MET cc_start: 0.7565 (mmm) cc_final: 0.7295 (mmm) REVERT: D 278 VAL cc_start: 0.7831 (m) cc_final: 0.7541 (p) REVERT: D 400 ILE cc_start: 0.8747 (pt) cc_final: 0.8547 (pt) REVERT: D 431 HIS cc_start: 0.6582 (m170) cc_final: 0.6052 (m170) REVERT: D 444 LEU cc_start: 0.6852 (tt) cc_final: 0.6497 (tt) REVERT: D 456 ILE cc_start: 0.8905 (mm) cc_final: 0.8198 (pt) REVERT: E 62 ILE cc_start: 0.8218 (mm) cc_final: 0.7944 (mm) REVERT: E 109 MET cc_start: 0.6186 (tpt) cc_final: 0.5835 (mmm) REVERT: E 167 LEU cc_start: 0.8297 (mp) cc_final: 0.7296 (mt) REVERT: F 157 TYR cc_start: 0.6405 (t80) cc_final: 0.5880 (t80) REVERT: F 418 GLN cc_start: 0.7084 (mm-40) cc_final: 0.6610 (mt0) REVERT: G 50 LEU cc_start: 0.8066 (tt) cc_final: 0.7741 (tp) REVERT: G 253 VAL cc_start: 0.7928 (t) cc_final: 0.7660 (t) REVERT: G 303 THR cc_start: 0.7649 (p) cc_final: 0.7430 (p) REVERT: G 659 ILE cc_start: 0.4239 (tt) cc_final: 0.3985 (tt) REVERT: G 691 ILE cc_start: 0.7267 (tt) cc_final: 0.6112 (tt) REVERT: H 13 ILE cc_start: 0.8886 (mm) cc_final: 0.8644 (mm) REVERT: H 55 LEU cc_start: 0.8332 (mt) cc_final: 0.8079 (mt) REVERT: H 165 LEU cc_start: 0.8714 (mp) cc_final: 0.8485 (mp) REVERT: I 66 LEU cc_start: 0.8603 (mt) cc_final: 0.8219 (mt) REVERT: I 73 THR cc_start: 0.8212 (p) cc_final: 0.7452 (p) REVERT: I 77 LEU cc_start: 0.7616 (tt) cc_final: 0.7276 (tt) REVERT: I 153 ILE cc_start: 0.7565 (pp) cc_final: 0.7213 (pp) REVERT: I 177 THR cc_start: 0.8238 (p) cc_final: 0.7432 (p) REVERT: I 190 LEU cc_start: 0.9030 (mt) cc_final: 0.8659 (mt) REVERT: P 100 LEU cc_start: 0.7706 (mp) cc_final: 0.7498 (mp) REVERT: Q 112 MET cc_start: 0.6169 (mmm) cc_final: 0.5603 (tpp) REVERT: Q 141 ASN cc_start: 0.6857 (m-40) cc_final: 0.6639 (m110) REVERT: T 110 LEU cc_start: 0.6725 (tp) cc_final: 0.5160 (tp) REVERT: V 55 LYS cc_start: 0.8372 (mmtm) cc_final: 0.7625 (mmtm) REVERT: V 86 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7985 (ttmt) REVERT: W 82 VAL cc_start: 0.9120 (t) cc_final: 0.8805 (p) REVERT: Z 79 LYS cc_start: 0.6986 (ttpt) cc_final: 0.6119 (tptt) REVERT: q 74 PHE cc_start: 0.3379 (t80) cc_final: 0.3086 (t80) outliers start: 10 outliers final: 1 residues processed: 1475 average time/residue: 0.5158 time to fit residues: 1182.2511 Evaluate side-chains 829 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 828 time to evaluate : 3.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 343 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 319 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 369 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 179 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN E 58 ASN E 73 HIS E 86 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN F 168 ASN F 270 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN G 221 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN G 444 HIS G 460 HIS ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 571 HIS G 604 GLN ** G 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 124 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN ** I 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 147 ASN P 154 GLN ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 341 GLN P 356 HIS ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 HIS S 48 HIS ** T 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 HIS V 41 HIS V 50 GLN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN W 105 HIS X 30 HIS ** X 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 HIS ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 GLN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 GLN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 31 ASN ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.081070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.064931 restraints weight = 177232.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066673 restraints weight = 117918.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.067840 restraints weight = 87608.417| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 34578 Z= 0.302 Angle : 1.115 66.611 46909 Z= 0.482 Chirality : 0.052 0.280 5135 Planarity : 0.007 0.089 5952 Dihedral : 8.571 149.145 4761 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 24.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.33 % Allowed : 5.46 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.12), residues: 4127 helix: -0.05 (0.11), residues: 1858 sheet: -1.11 (0.28), residues: 341 loop : -1.34 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP Q 97 HIS 0.017 0.002 HIS G 66 PHE 0.035 0.003 PHE H 223 TYR 0.052 0.003 TYR B 170 ARG 0.015 0.001 ARG a 59 Details of bonding type rmsd hydrogen bonds : bond 0.06060 ( 1439) hydrogen bonds : angle 6.04653 ( 4155) metal coordination : bond 0.04516 ( 33) metal coordination : angle 15.49029 ( 81) SS BOND : bond 0.00355 ( 3) SS BOND : angle 1.43651 ( 6) covalent geometry : bond 0.00645 (34542) covalent geometry : angle 0.91085 (46822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 958 time to evaluate : 3.563 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6879 (ptm) cc_final: 0.6556 (ppp) REVERT: A 10 ASN cc_start: 0.9142 (m-40) cc_final: 0.7681 (t0) REVERT: A 88 MET cc_start: 0.8631 (tpp) cc_final: 0.7859 (ttp) REVERT: B 103 GLU cc_start: 0.9110 (tp30) cc_final: 0.8873 (tp30) REVERT: B 106 HIS cc_start: 0.8594 (m-70) cc_final: 0.8213 (m-70) REVERT: B 117 PHE cc_start: 0.9594 (m-80) cc_final: 0.9145 (m-10) REVERT: B 129 ASP cc_start: 0.7384 (m-30) cc_final: 0.7163 (m-30) REVERT: B 173 TYR cc_start: 0.8070 (m-80) cc_final: 0.7819 (m-80) REVERT: B 201 LEU cc_start: 0.9765 (tp) cc_final: 0.9519 (tp) REVERT: C 104 ASN cc_start: 0.8899 (m110) cc_final: 0.8679 (m110) REVERT: C 189 ASP cc_start: 0.8188 (t0) cc_final: 0.7515 (t70) REVERT: C 227 GLN cc_start: 0.8542 (tt0) cc_final: 0.7729 (tt0) REVERT: D 145 MET cc_start: 0.8625 (mtt) cc_final: 0.8372 (mtt) REVERT: D 185 MET cc_start: 0.9237 (tpp) cc_final: 0.8901 (tpp) REVERT: D 204 PHE cc_start: 0.8349 (m-10) cc_final: 0.7977 (m-10) REVERT: D 222 MET cc_start: 0.9091 (ptm) cc_final: 0.8722 (ptt) REVERT: D 268 TRP cc_start: 0.8901 (t-100) cc_final: 0.8388 (t-100) REVERT: D 286 TYR cc_start: 0.8895 (m-80) cc_final: 0.8596 (m-80) REVERT: D 443 MET cc_start: 0.9017 (mmp) cc_final: 0.8544 (mmp) REVERT: E 87 ARG cc_start: 0.8043 (mmt180) cc_final: 0.7739 (mmt180) REVERT: E 131 ILE cc_start: 0.9122 (mm) cc_final: 0.8910 (mp) REVERT: E 165 ASP cc_start: 0.8564 (t0) cc_final: 0.8325 (t0) REVERT: E 238 LYS cc_start: 0.6955 (mtmt) cc_final: 0.4531 (mttt) REVERT: F 42 PHE cc_start: 0.8788 (t80) cc_final: 0.8556 (t80) REVERT: F 136 HIS cc_start: 0.8270 (m-70) cc_final: 0.8008 (m-70) REVERT: F 262 PHE cc_start: 0.8330 (t80) cc_final: 0.8080 (t80) REVERT: F 446 LEU cc_start: 0.9574 (tp) cc_final: 0.9358 (tp) REVERT: G 65 TYR cc_start: 0.8808 (t80) cc_final: 0.8545 (t80) REVERT: G 66 HIS cc_start: 0.8005 (t-90) cc_final: 0.7652 (t70) REVERT: G 117 MET cc_start: 0.8977 (tpp) cc_final: 0.8705 (tpp) REVERT: G 218 LEU cc_start: 0.9329 (mt) cc_final: 0.9085 (mt) REVERT: G 306 MET cc_start: 0.8292 (ttm) cc_final: 0.8090 (ttm) REVERT: G 333 PHE cc_start: 0.8653 (m-80) cc_final: 0.7118 (m-80) REVERT: G 387 LEU cc_start: 0.8666 (mt) cc_final: 0.8416 (mt) REVERT: G 513 MET cc_start: 0.8627 (pmm) cc_final: 0.8408 (pmm) REVERT: G 626 LEU cc_start: 0.8861 (tp) cc_final: 0.8576 (tp) REVERT: G 639 LEU cc_start: 0.9080 (tt) cc_final: 0.8235 (mp) REVERT: G 643 ARG cc_start: 0.8932 (mmt90) cc_final: 0.7829 (tmm-80) REVERT: H 40 VAL cc_start: 0.9051 (p) cc_final: 0.8788 (p) REVERT: H 57 MET cc_start: 0.7797 (mtt) cc_final: 0.7437 (mtt) REVERT: H 61 MET cc_start: 0.8353 (ttp) cc_final: 0.7932 (tmm) REVERT: H 79 LEU cc_start: 0.9625 (tp) cc_final: 0.9410 (tp) REVERT: H 83 LEU cc_start: 0.9377 (mt) cc_final: 0.9007 (mt) REVERT: H 86 TRP cc_start: 0.8829 (m100) cc_final: 0.8615 (m100) REVERT: H 143 GLU cc_start: 0.9209 (tp30) cc_final: 0.8885 (tp30) REVERT: H 146 MET cc_start: 0.8395 (mtt) cc_final: 0.8039 (mtt) REVERT: H 225 MET cc_start: 0.9438 (mtm) cc_final: 0.9175 (mmm) REVERT: H 281 ARG cc_start: 0.8924 (ttm170) cc_final: 0.8650 (ttp-170) REVERT: H 282 TYR cc_start: 0.8891 (t80) cc_final: 0.8518 (t80) REVERT: H 284 GLN cc_start: 0.9501 (mm110) cc_final: 0.8740 (mm-40) REVERT: H 288 LEU cc_start: 0.9653 (mm) cc_final: 0.9346 (mm) REVERT: I 159 GLN cc_start: 0.9102 (tp40) cc_final: 0.8715 (tp40) REVERT: I 177 THR cc_start: 0.8954 (p) cc_final: 0.8208 (p) REVERT: I 182 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8935 (mt-10) REVERT: P 95 ARG cc_start: 0.9190 (mtp180) cc_final: 0.8760 (mtm-85) REVERT: P 233 PHE cc_start: 0.7232 (m-80) cc_final: 0.6860 (m-80) REVERT: P 328 MET cc_start: 0.7313 (pmm) cc_final: 0.6735 (pmm) REVERT: P 335 LEU cc_start: 0.8287 (mt) cc_final: 0.8026 (tp) REVERT: P 346 GLU cc_start: 0.8922 (pm20) cc_final: 0.8720 (pm20) REVERT: P 348 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7710 (mmtt) REVERT: Q 71 HIS cc_start: 0.9014 (m90) cc_final: 0.8653 (m-70) REVERT: Q 112 MET cc_start: 0.8066 (mmm) cc_final: 0.7498 (mmm) REVERT: Q 141 ASN cc_start: 0.9154 (m-40) cc_final: 0.8911 (m110) REVERT: Q 164 PHE cc_start: 0.8577 (m-80) cc_final: 0.8341 (m-80) REVERT: S 81 ASN cc_start: 0.8738 (t0) cc_final: 0.8502 (t0) REVERT: T 113 LEU cc_start: 0.9114 (mm) cc_final: 0.8483 (mm) REVERT: V 93 LYS cc_start: 0.9298 (mtmm) cc_final: 0.9039 (mttt) REVERT: V 94 MET cc_start: 0.8683 (mmm) cc_final: 0.8347 (mmm) REVERT: W 69 MET cc_start: 0.9712 (tpp) cc_final: 0.9466 (tpp) REVERT: W 78 ASP cc_start: 0.8971 (t70) cc_final: 0.8688 (t0) REVERT: W 105 HIS cc_start: 0.8289 (m-70) cc_final: 0.7804 (m90) REVERT: X 32 TYR cc_start: 0.7975 (t80) cc_final: 0.6958 (t80) REVERT: Z 51 MET cc_start: 0.9063 (tmm) cc_final: 0.8757 (tmm) REVERT: a 9 LEU cc_start: 0.8869 (pp) cc_final: 0.8513 (mt) REVERT: a 11 ILE cc_start: 0.8629 (mt) cc_final: 0.8406 (mm) REVERT: a 15 CYS cc_start: 0.9345 (m) cc_final: 0.9026 (m) REVERT: a 48 MET cc_start: 0.8919 (ttm) cc_final: 0.8457 (ttm) REVERT: q 127 TYR cc_start: 0.9026 (p90) cc_final: 0.8595 (p90) REVERT: s 42 THR cc_start: 0.7607 (p) cc_final: 0.7217 (p) REVERT: s 52 LEU cc_start: 0.7618 (mt) cc_final: 0.7330 (mt) outliers start: 12 outliers final: 4 residues processed: 965 average time/residue: 0.4757 time to fit residues: 733.8783 Evaluate side-chains 697 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 693 time to evaluate : 3.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 324 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 39 optimal weight: 0.0000 chunk 347 optimal weight: 4.9990 chunk 289 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 270 optimal weight: 1.9990 chunk 402 optimal weight: 20.0000 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN D 270 ASN D 381 HIS E 122 ASN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 ASN ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 ASN ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 269 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN X 124 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.082637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.066689 restraints weight = 174012.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.068493 restraints weight = 112352.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.069790 restraints weight = 82908.193| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 34578 Z= 0.167 Angle : 0.920 59.278 46909 Z= 0.376 Chirality : 0.046 0.236 5135 Planarity : 0.006 0.081 5952 Dihedral : 8.189 144.521 4761 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.28 % Allowed : 3.53 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 4127 helix: 0.47 (0.12), residues: 1865 sheet: -0.94 (0.28), residues: 331 loop : -1.04 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP H 118 HIS 0.013 0.001 HIS q 91 PHE 0.025 0.002 PHE D 458 TYR 0.028 0.002 TYR X 32 ARG 0.009 0.001 ARG D 271 Details of bonding type rmsd hydrogen bonds : bond 0.05027 ( 1439) hydrogen bonds : angle 5.44804 ( 4155) metal coordination : bond 0.02204 ( 33) metal coordination : angle 13.80984 ( 81) SS BOND : bond 0.00465 ( 3) SS BOND : angle 1.44872 ( 6) covalent geometry : bond 0.00375 (34542) covalent geometry : angle 0.71937 (46822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 916 time to evaluate : 3.606 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: 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: 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: 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: A 1 MET cc_start: 0.6741 (ptm) cc_final: 0.6503 (ppp) REVERT: A 55 PHE cc_start: 0.6390 (m-80) cc_final: 0.6177 (m-80) REVERT: A 88 MET cc_start: 0.8793 (tpp) cc_final: 0.8152 (ttt) REVERT: B 117 PHE cc_start: 0.9560 (m-80) cc_final: 0.9078 (m-10) REVERT: B 133 VAL cc_start: 0.9263 (p) cc_final: 0.8940 (p) REVERT: B 173 TYR cc_start: 0.8055 (m-80) cc_final: 0.7525 (m-80) REVERT: B 176 SER cc_start: 0.9107 (m) cc_final: 0.8876 (p) REVERT: B 211 LYS cc_start: 0.8727 (mttm) cc_final: 0.7689 (mttt) REVERT: C 104 ASN cc_start: 0.8757 (m110) cc_final: 0.8473 (m-40) REVERT: C 166 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8353 (mt-10) REVERT: C 230 ARG cc_start: 0.8074 (mpt-90) cc_final: 0.7308 (mtt90) REVERT: D 185 MET cc_start: 0.9211 (tpp) cc_final: 0.8863 (tpp) REVERT: D 200 PHE cc_start: 0.8690 (t80) cc_final: 0.8315 (t80) REVERT: D 203 MET cc_start: 0.9463 (mmp) cc_final: 0.9185 (mmp) REVERT: D 210 MET cc_start: 0.9219 (mtm) cc_final: 0.8880 (mtm) REVERT: D 214 TYR cc_start: 0.8613 (m-10) cc_final: 0.8115 (m-80) REVERT: D 251 PHE cc_start: 0.8976 (t80) cc_final: 0.8645 (t80) REVERT: D 257 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8564 (mt-10) REVERT: D 286 TYR cc_start: 0.8876 (m-80) cc_final: 0.8368 (m-80) REVERT: D 443 MET cc_start: 0.9134 (mmp) cc_final: 0.8615 (mmp) REVERT: D 456 ILE cc_start: 0.9291 (mm) cc_final: 0.8641 (pt) REVERT: E 109 MET cc_start: 0.7763 (tpt) cc_final: 0.6271 (tpt) REVERT: E 118 TYR cc_start: 0.8267 (m-80) cc_final: 0.8022 (m-80) REVERT: F 62 TRP cc_start: 0.7734 (t60) cc_final: 0.7387 (t60) REVERT: F 136 HIS cc_start: 0.8257 (m-70) cc_final: 0.8020 (m-70) REVERT: F 149 MET cc_start: 0.7103 (mmt) cc_final: 0.6762 (mmt) REVERT: F 262 PHE cc_start: 0.8445 (t80) cc_final: 0.7973 (t80) REVERT: G 39 GLN cc_start: 0.8836 (tp40) cc_final: 0.8222 (tm-30) REVERT: G 50 LEU cc_start: 0.9351 (tt) cc_final: 0.8953 (tt) REVERT: G 218 LEU cc_start: 0.9257 (mt) cc_final: 0.9006 (mt) REVERT: G 387 LEU cc_start: 0.8776 (mt) cc_final: 0.8543 (mt) REVERT: G 473 MET cc_start: 0.8209 (ptm) cc_final: 0.7863 (ttp) REVERT: G 626 LEU cc_start: 0.8806 (tp) cc_final: 0.8499 (tp) REVERT: G 643 ARG cc_start: 0.8894 (mmt90) cc_final: 0.7866 (tmm-80) REVERT: H 2 PHE cc_start: 0.7281 (t80) cc_final: 0.7042 (t80) REVERT: H 17 MET cc_start: 0.9472 (tmm) cc_final: 0.8460 (ttp) REVERT: H 31 MET cc_start: 0.8785 (ttm) cc_final: 0.8483 (mmm) REVERT: H 61 MET cc_start: 0.8188 (ttp) cc_final: 0.7829 (tmm) REVERT: H 79 LEU cc_start: 0.9585 (tp) cc_final: 0.9376 (tp) REVERT: H 83 LEU cc_start: 0.9452 (mt) cc_final: 0.9141 (mt) REVERT: H 134 ARG cc_start: 0.8530 (mtp180) cc_final: 0.8089 (mtp180) REVERT: H 143 GLU cc_start: 0.9057 (tp30) cc_final: 0.8825 (tp30) REVERT: H 146 MET cc_start: 0.8678 (mtt) cc_final: 0.8339 (mtt) REVERT: H 225 MET cc_start: 0.9262 (mtm) cc_final: 0.9035 (mmt) REVERT: H 234 MET cc_start: 0.9417 (tpp) cc_final: 0.9169 (tpp) REVERT: H 288 LEU cc_start: 0.9580 (mm) cc_final: 0.9217 (mm) REVERT: H 318 MET cc_start: 0.7479 (tpt) cc_final: 0.6562 (tmm) REVERT: I 48 VAL cc_start: 0.4544 (m) cc_final: 0.4056 (t) REVERT: I 73 THR cc_start: 0.9555 (p) cc_final: 0.9128 (p) REVERT: I 159 GLN cc_start: 0.8998 (tp40) cc_final: 0.8492 (tp40) REVERT: I 179 THR cc_start: 0.9028 (p) cc_final: 0.8739 (p) REVERT: P 233 PHE cc_start: 0.7298 (m-80) cc_final: 0.6976 (m-80) REVERT: P 328 MET cc_start: 0.7324 (pmm) cc_final: 0.6778 (pmm) REVERT: P 335 LEU cc_start: 0.8330 (mt) cc_final: 0.8113 (mt) REVERT: P 347 LEU cc_start: 0.8986 (mp) cc_final: 0.8736 (mp) REVERT: P 348 LYS cc_start: 0.8148 (mmtm) cc_final: 0.6881 (ttmt) REVERT: Q 71 HIS cc_start: 0.9066 (m90) cc_final: 0.8784 (m-70) REVERT: Q 87 MET cc_start: 0.9290 (mmp) cc_final: 0.9070 (mmp) REVERT: Q 98 LYS cc_start: 0.9242 (tttp) cc_final: 0.9024 (tptt) REVERT: Q 111 LEU cc_start: 0.9054 (pp) cc_final: 0.8800 (pp) REVERT: Q 112 MET cc_start: 0.8116 (mmm) cc_final: 0.7704 (mmm) REVERT: Q 156 LYS cc_start: 0.8207 (mmpt) cc_final: 0.7951 (mmmt) REVERT: Q 164 PHE cc_start: 0.8266 (m-80) cc_final: 0.7917 (m-80) REVERT: S 81 ASN cc_start: 0.8724 (t0) cc_final: 0.8469 (t0) REVERT: T 80 LYS cc_start: 0.8498 (tmtt) cc_final: 0.7869 (mptt) REVERT: T 113 LEU cc_start: 0.9196 (mm) cc_final: 0.8750 (mm) REVERT: T 130 ILE cc_start: 0.7925 (mp) cc_final: 0.7160 (mp) REVERT: T 133 ILE cc_start: 0.8759 (pt) cc_final: 0.8371 (pt) REVERT: V 93 LYS cc_start: 0.9430 (mtmm) cc_final: 0.9190 (mttp) REVERT: W 69 MET cc_start: 0.9629 (tpp) cc_final: 0.9383 (tpp) REVERT: W 78 ASP cc_start: 0.8907 (t70) cc_final: 0.8631 (t0) REVERT: W 92 GLU cc_start: 0.9401 (tp30) cc_final: 0.9138 (tp30) REVERT: W 95 GLU cc_start: 0.8243 (tp30) cc_final: 0.7849 (tp30) REVERT: W 107 MET cc_start: 0.8906 (mmt) cc_final: 0.8590 (mmm) REVERT: W 127 MET cc_start: 0.7250 (tpp) cc_final: 0.6907 (mmm) REVERT: Z 10 MET cc_start: 0.8212 (mmm) cc_final: 0.7511 (mmt) REVERT: Z 21 TYR cc_start: 0.8249 (p90) cc_final: 0.8007 (p90) REVERT: a 9 LEU cc_start: 0.8803 (pp) cc_final: 0.8482 (mt) REVERT: a 11 ILE cc_start: 0.8626 (mt) cc_final: 0.8417 (mm) REVERT: a 15 CYS cc_start: 0.9318 (m) cc_final: 0.8997 (m) REVERT: a 37 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7292 (mtm-85) REVERT: a 48 MET cc_start: 0.8946 (ttm) cc_final: 0.8173 (ttm) REVERT: q 127 TYR cc_start: 0.9038 (p90) cc_final: 0.8014 (p90) REVERT: r 93 LYS cc_start: 0.8276 (mppt) cc_final: 0.7786 (mmmt) outliers start: 10 outliers final: 1 residues processed: 922 average time/residue: 0.4647 time to fit residues: 690.1296 Evaluate side-chains 693 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 692 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 40 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 386 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 chunk 293 optimal weight: 0.3980 chunk 294 optimal weight: 2.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 131 GLN D 147 ASN D 149 GLN E 58 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN F 303 HIS ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 ASN G 495 ASN G 498 GLN ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 ASN P 166 HIS ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 129 HIS X 103 GLN Z 54 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.079505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.064115 restraints weight = 179170.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.065952 restraints weight = 115958.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067293 restraints weight = 84490.074| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34578 Z= 0.196 Angle : 0.944 71.503 46909 Z= 0.374 Chirality : 0.046 0.227 5135 Planarity : 0.006 0.075 5952 Dihedral : 8.167 148.002 4761 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.11 % Allowed : 4.11 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.51 (0.13), residues: 4127 helix: 0.44 (0.12), residues: 1884 sheet: -0.88 (0.29), residues: 326 loop : -0.96 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP V 97 HIS 0.011 0.002 HIS q 91 PHE 0.036 0.002 PHE A 92 TYR 0.031 0.002 TYR B 170 ARG 0.008 0.001 ARG H 274 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 1439) hydrogen bonds : angle 5.37399 ( 4155) metal coordination : bond 0.02525 ( 33) metal coordination : angle 14.88306 ( 81) SS BOND : bond 0.00743 ( 3) SS BOND : angle 1.67403 ( 6) covalent geometry : bond 0.00438 (34542) covalent geometry : angle 0.71426 (46822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 872 time to evaluate : 3.629 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6887 (ptm) cc_final: 0.6516 (ppp) REVERT: A 88 MET cc_start: 0.8542 (tpp) cc_final: 0.7124 (tpt) REVERT: B 114 MET cc_start: 0.9037 (ptp) cc_final: 0.8771 (ptm) REVERT: B 133 VAL cc_start: 0.9529 (p) cc_final: 0.9320 (p) REVERT: B 149 TYR cc_start: 0.9244 (t80) cc_final: 0.8669 (t80) REVERT: B 173 TYR cc_start: 0.8241 (m-80) cc_final: 0.7734 (m-80) REVERT: B 206 LEU cc_start: 0.9373 (tt) cc_final: 0.9165 (tt) REVERT: C 104 ASN cc_start: 0.8689 (m110) cc_final: 0.8458 (m-40) REVERT: C 164 TRP cc_start: 0.8480 (m-10) cc_final: 0.8180 (m-10) REVERT: C 172 MET cc_start: 0.8643 (tpp) cc_final: 0.7604 (tpp) REVERT: C 230 ARG cc_start: 0.7630 (mpt-90) cc_final: 0.7358 (mtt90) REVERT: D 185 MET cc_start: 0.9133 (tpp) cc_final: 0.8841 (tpp) REVERT: D 200 PHE cc_start: 0.8491 (t80) cc_final: 0.8288 (t80) REVERT: D 210 MET cc_start: 0.9290 (mtm) cc_final: 0.8811 (mtm) REVERT: D 251 PHE cc_start: 0.9039 (t80) cc_final: 0.8680 (t80) REVERT: D 257 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8583 (mt-10) REVERT: D 286 TYR cc_start: 0.9028 (m-80) cc_final: 0.8526 (m-80) REVERT: D 456 ILE cc_start: 0.9314 (mm) cc_final: 0.8708 (pt) REVERT: E 109 MET cc_start: 0.7200 (tpt) cc_final: 0.5765 (tpt) REVERT: E 118 TYR cc_start: 0.8423 (m-80) cc_final: 0.7878 (m-80) REVERT: E 184 MET cc_start: 0.7773 (ptm) cc_final: 0.7559 (ptt) REVERT: E 242 PHE cc_start: 0.7294 (p90) cc_final: 0.6677 (p90) REVERT: F 62 TRP cc_start: 0.7805 (t60) cc_final: 0.7524 (t60) REVERT: F 136 HIS cc_start: 0.8345 (m-70) cc_final: 0.8074 (m-70) REVERT: F 149 MET cc_start: 0.7294 (mmt) cc_final: 0.6839 (mmt) REVERT: F 262 PHE cc_start: 0.8565 (t80) cc_final: 0.8077 (t80) REVERT: G 39 GLN cc_start: 0.8814 (tp40) cc_final: 0.8211 (tm-30) REVERT: G 53 CYS cc_start: 0.8641 (t) cc_final: 0.8419 (t) REVERT: G 77 MET cc_start: 0.8950 (tpt) cc_final: 0.8662 (tpp) REVERT: G 218 LEU cc_start: 0.9230 (mt) cc_final: 0.8968 (mt) REVERT: G 278 HIS cc_start: 0.8895 (t-90) cc_final: 0.8598 (t-170) REVERT: G 354 LEU cc_start: 0.9767 (tp) cc_final: 0.9516 (tt) REVERT: G 387 LEU cc_start: 0.8832 (mt) cc_final: 0.8554 (mt) REVERT: G 473 MET cc_start: 0.8238 (ptm) cc_final: 0.7855 (ttp) REVERT: G 591 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7545 (tm-30) REVERT: G 626 LEU cc_start: 0.8760 (tp) cc_final: 0.8443 (tp) REVERT: G 643 ARG cc_start: 0.8972 (mmt90) cc_final: 0.7995 (tmm-80) REVERT: H 17 MET cc_start: 0.9461 (tmm) cc_final: 0.8168 (tmm) REVERT: H 31 MET cc_start: 0.8775 (ttm) cc_final: 0.8315 (mmm) REVERT: H 53 MET cc_start: 0.8771 (mmt) cc_final: 0.8465 (ttt) REVERT: H 71 PHE cc_start: 0.7369 (t80) cc_final: 0.6949 (t80) REVERT: H 79 LEU cc_start: 0.9519 (tp) cc_final: 0.9277 (tp) REVERT: H 83 LEU cc_start: 0.9471 (mt) cc_final: 0.9138 (mt) REVERT: H 134 ARG cc_start: 0.8612 (mtp180) cc_final: 0.8286 (mtp180) REVERT: H 139 THR cc_start: 0.9575 (p) cc_final: 0.9249 (p) REVERT: H 181 MET cc_start: 0.8684 (mtm) cc_final: 0.8480 (mtm) REVERT: H 183 MET cc_start: 0.9215 (mtt) cc_final: 0.8824 (mtt) REVERT: H 192 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8602 (tm-30) REVERT: H 225 MET cc_start: 0.9200 (mtm) cc_final: 0.8937 (mmt) REVERT: H 234 MET cc_start: 0.9556 (mmp) cc_final: 0.9108 (mmm) REVERT: H 281 ARG cc_start: 0.8474 (ptt180) cc_final: 0.8173 (ptp-170) REVERT: H 284 GLN cc_start: 0.9468 (mm110) cc_final: 0.9119 (mm110) REVERT: H 288 LEU cc_start: 0.9672 (mm) cc_final: 0.9279 (mm) REVERT: I 48 VAL cc_start: 0.4693 (m) cc_final: 0.4229 (t) REVERT: I 73 THR cc_start: 0.9578 (p) cc_final: 0.9099 (p) REVERT: I 159 GLN cc_start: 0.9059 (tp40) cc_final: 0.8616 (tp40) REVERT: P 48 ARG cc_start: 0.6110 (tpp80) cc_final: 0.5595 (tpp80) REVERT: P 233 PHE cc_start: 0.7332 (m-80) cc_final: 0.7014 (m-80) REVERT: P 347 LEU cc_start: 0.9020 (mp) cc_final: 0.8767 (mp) REVERT: P 348 LYS cc_start: 0.8133 (mmtm) cc_final: 0.6876 (mttp) REVERT: Q 112 MET cc_start: 0.8348 (mmm) cc_final: 0.7983 (mmm) REVERT: Q 114 TRP cc_start: 0.8869 (m-10) cc_final: 0.8513 (m-10) REVERT: Q 128 PHE cc_start: 0.7699 (m-10) cc_final: 0.5866 (m-10) REVERT: Q 141 ASN cc_start: 0.9289 (m110) cc_final: 0.8692 (m110) REVERT: S 20 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7614 (mtm180) REVERT: S 81 ASN cc_start: 0.8709 (t0) cc_final: 0.8410 (t0) REVERT: T 80 LYS cc_start: 0.8678 (tmtt) cc_final: 0.8114 (mptt) REVERT: T 113 LEU cc_start: 0.9196 (mm) cc_final: 0.8808 (mm) REVERT: T 132 ASP cc_start: 0.8611 (m-30) cc_final: 0.8360 (m-30) REVERT: V 28 TYR cc_start: 0.8760 (m-80) cc_final: 0.8538 (m-80) REVERT: W 69 MET cc_start: 0.9664 (tpp) cc_final: 0.9463 (tpp) REVERT: W 78 ASP cc_start: 0.8961 (t70) cc_final: 0.8660 (t0) REVERT: W 94 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8842 (mm-40) REVERT: W 107 MET cc_start: 0.8864 (mmt) cc_final: 0.8474 (mmm) REVERT: W 127 MET cc_start: 0.7418 (tpp) cc_final: 0.7065 (mmm) REVERT: X 83 THR cc_start: 0.9312 (m) cc_final: 0.8925 (m) REVERT: Z 10 MET cc_start: 0.8481 (mmm) cc_final: 0.7881 (mmt) REVERT: Z 21 TYR cc_start: 0.8239 (p90) cc_final: 0.7965 (p90) REVERT: a 9 LEU cc_start: 0.8853 (pp) cc_final: 0.8568 (mt) REVERT: a 37 ARG cc_start: 0.8020 (mtm110) cc_final: 0.6870 (mtm-85) REVERT: a 45 TRP cc_start: 0.8534 (t-100) cc_final: 0.8331 (t60) REVERT: q 127 TYR cc_start: 0.9141 (p90) cc_final: 0.8170 (p90) REVERT: r 93 LYS cc_start: 0.8500 (mppt) cc_final: 0.7902 (mmmt) REVERT: r 101 MET cc_start: 0.8112 (mtp) cc_final: 0.7792 (ptp) REVERT: r 109 ASP cc_start: 0.7891 (p0) cc_final: 0.7291 (p0) outliers start: 4 outliers final: 1 residues processed: 876 average time/residue: 0.4610 time to fit residues: 650.8045 Evaluate side-chains 668 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 667 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 165 optimal weight: 7.9990 chunk 259 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 109 optimal weight: 0.0370 chunk 233 optimal weight: 8.9990 chunk 274 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 227 optimal weight: 0.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 131 GLN D 149 GLN E 58 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 ASN W 29 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 9 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.079745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064156 restraints weight = 177696.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.065985 restraints weight = 115960.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.067265 restraints weight = 85294.358| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34578 Z= 0.164 Angle : 0.931 76.264 46909 Z= 0.358 Chirality : 0.045 0.204 5135 Planarity : 0.005 0.064 5952 Dihedral : 7.968 145.375 4761 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4127 helix: 0.50 (0.12), residues: 1888 sheet: -0.84 (0.29), residues: 314 loop : -0.86 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP V 97 HIS 0.009 0.001 HIS X 31 PHE 0.027 0.002 PHE C 197 TYR 0.033 0.002 TYR F 46 ARG 0.012 0.001 ARG R 51 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 1439) hydrogen bonds : angle 5.25197 ( 4155) metal coordination : bond 0.02252 ( 33) metal coordination : angle 15.12307 ( 81) SS BOND : bond 0.00457 ( 3) SS BOND : angle 1.37717 ( 6) covalent geometry : bond 0.00374 (34542) covalent geometry : angle 0.68713 (46822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 864 time to evaluate : 3.757 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6944 (ptm) cc_final: 0.6658 (ppp) REVERT: A 88 MET cc_start: 0.8791 (tpp) cc_final: 0.7475 (tpt) REVERT: A 92 PHE cc_start: 0.7982 (m-10) cc_final: 0.7721 (m-10) REVERT: A 98 LEU cc_start: 0.8670 (mm) cc_final: 0.8221 (tp) REVERT: B 161 MET cc_start: 0.8807 (mmm) cc_final: 0.8270 (tpt) REVERT: B 173 TYR cc_start: 0.8224 (m-80) cc_final: 0.7487 (m-80) REVERT: B 201 LEU cc_start: 0.9380 (tp) cc_final: 0.9104 (tp) REVERT: C 104 ASN cc_start: 0.8684 (m110) cc_final: 0.8422 (m-40) REVERT: C 165 TYR cc_start: 0.9245 (m-10) cc_final: 0.9043 (m-10) REVERT: C 172 MET cc_start: 0.8570 (tpp) cc_final: 0.7795 (tpp) REVERT: C 228 GLU cc_start: 0.8272 (pt0) cc_final: 0.8000 (pt0) REVERT: C 229 PHE cc_start: 0.9417 (t80) cc_final: 0.8927 (t80) REVERT: C 230 ARG cc_start: 0.7745 (mpt-90) cc_final: 0.7530 (mtt90) REVERT: D 145 MET cc_start: 0.8585 (mpp) cc_final: 0.8055 (mtm) REVERT: D 185 MET cc_start: 0.9396 (tpp) cc_final: 0.9184 (tpp) REVERT: D 190 HIS cc_start: 0.8610 (t-170) cc_final: 0.8405 (t70) REVERT: D 203 MET cc_start: 0.9405 (mmp) cc_final: 0.9141 (mmp) REVERT: D 210 MET cc_start: 0.9331 (mtm) cc_final: 0.8903 (mtm) REVERT: D 222 MET cc_start: 0.8784 (ptm) cc_final: 0.8523 (ptt) REVERT: D 251 PHE cc_start: 0.9114 (t80) cc_final: 0.8738 (t80) REVERT: D 257 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8783 (mt-10) REVERT: D 286 TYR cc_start: 0.9012 (m-80) cc_final: 0.8517 (m-80) REVERT: D 377 SER cc_start: 0.9500 (m) cc_final: 0.9198 (t) REVERT: D 443 MET cc_start: 0.9139 (mmp) cc_final: 0.8847 (mmp) REVERT: D 456 ILE cc_start: 0.9256 (mm) cc_final: 0.8780 (pt) REVERT: E 118 TYR cc_start: 0.8271 (m-80) cc_final: 0.7979 (m-80) REVERT: E 242 PHE cc_start: 0.7189 (p90) cc_final: 0.6555 (p90) REVERT: F 62 TRP cc_start: 0.7722 (t60) cc_final: 0.7381 (t60) REVERT: F 136 HIS cc_start: 0.8317 (m-70) cc_final: 0.8044 (m-70) REVERT: F 262 PHE cc_start: 0.8617 (t80) cc_final: 0.8169 (t80) REVERT: F 418 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8240 (mt0) REVERT: G 39 GLN cc_start: 0.8909 (tp40) cc_final: 0.8214 (tm-30) REVERT: G 53 CYS cc_start: 0.8618 (t) cc_final: 0.7881 (t) REVERT: G 77 MET cc_start: 0.9057 (tpt) cc_final: 0.8743 (tpp) REVERT: G 204 MET cc_start: 0.8197 (mtm) cc_final: 0.7865 (mtp) REVERT: G 218 LEU cc_start: 0.9291 (mt) cc_final: 0.9009 (mt) REVERT: G 254 MET cc_start: 0.8136 (mmt) cc_final: 0.7934 (mmm) REVERT: G 278 HIS cc_start: 0.8958 (t-90) cc_final: 0.8497 (t-170) REVERT: G 333 PHE cc_start: 0.8461 (m-80) cc_final: 0.8198 (m-10) REVERT: G 349 GLU cc_start: 0.8613 (pm20) cc_final: 0.7965 (pm20) REVERT: G 473 MET cc_start: 0.8266 (ptm) cc_final: 0.7911 (ttp) REVERT: G 579 MET cc_start: 0.8949 (mmm) cc_final: 0.8740 (tpt) REVERT: G 643 ARG cc_start: 0.8968 (mmt90) cc_final: 0.8014 (tmm-80) REVERT: H 17 MET cc_start: 0.9488 (tmm) cc_final: 0.8298 (tmm) REVERT: H 71 PHE cc_start: 0.7548 (t80) cc_final: 0.7035 (t80) REVERT: H 79 LEU cc_start: 0.9524 (tp) cc_final: 0.9306 (tp) REVERT: H 83 LEU cc_start: 0.9501 (mt) cc_final: 0.9201 (mt) REVERT: H 134 ARG cc_start: 0.8814 (mtp180) cc_final: 0.8515 (mtp-110) REVERT: H 183 MET cc_start: 0.9232 (mtt) cc_final: 0.8763 (mtt) REVERT: H 225 MET cc_start: 0.9221 (mtm) cc_final: 0.8920 (mmt) REVERT: H 238 THR cc_start: 0.9311 (m) cc_final: 0.9046 (p) REVERT: H 240 ILE cc_start: 0.9592 (mm) cc_final: 0.9220 (mm) REVERT: H 288 LEU cc_start: 0.9561 (mm) cc_final: 0.9054 (mm) REVERT: I 48 VAL cc_start: 0.4680 (m) cc_final: 0.4272 (t) REVERT: I 78 PHE cc_start: 0.9086 (m-80) cc_final: 0.8749 (m-80) REVERT: I 159 GLN cc_start: 0.9123 (tp40) cc_final: 0.8654 (tp40) REVERT: I 195 ASP cc_start: 0.9035 (m-30) cc_final: 0.8827 (m-30) REVERT: P 233 PHE cc_start: 0.7431 (m-80) cc_final: 0.7116 (m-80) REVERT: P 335 LEU cc_start: 0.8541 (mm) cc_final: 0.8258 (mp) REVERT: P 348 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7536 (mmtm) REVERT: Q 112 MET cc_start: 0.8372 (mmm) cc_final: 0.7941 (mmm) REVERT: Q 114 TRP cc_start: 0.8975 (m-10) cc_final: 0.8612 (m-10) REVERT: Q 122 SER cc_start: 0.9435 (p) cc_final: 0.9156 (m) REVERT: Q 126 LEU cc_start: 0.8910 (tp) cc_final: 0.8663 (tt) REVERT: Q 141 ASN cc_start: 0.9332 (m110) cc_final: 0.8662 (m110) REVERT: Q 156 LYS cc_start: 0.8123 (mmpt) cc_final: 0.7872 (mmmt) REVERT: Q 164 PHE cc_start: 0.8160 (m-80) cc_final: 0.7710 (m-80) REVERT: S 81 ASN cc_start: 0.8733 (t0) cc_final: 0.8416 (t0) REVERT: T 80 LYS cc_start: 0.8686 (tmmt) cc_final: 0.8249 (mptt) REVERT: T 113 LEU cc_start: 0.9145 (mm) cc_final: 0.8743 (mm) REVERT: T 133 ILE cc_start: 0.8883 (pt) cc_final: 0.8437 (pt) REVERT: V 93 LYS cc_start: 0.9402 (mtmm) cc_final: 0.8958 (mttp) REVERT: W 78 ASP cc_start: 0.8954 (t70) cc_final: 0.8650 (t0) REVERT: W 94 GLN cc_start: 0.9244 (mm-40) cc_final: 0.9002 (mm-40) REVERT: W 127 MET cc_start: 0.7407 (tpp) cc_final: 0.7104 (mmm) REVERT: Z 10 MET cc_start: 0.8586 (mmm) cc_final: 0.7983 (mmt) REVERT: Z 21 TYR cc_start: 0.8274 (p90) cc_final: 0.7966 (p90) REVERT: a 9 LEU cc_start: 0.8886 (pp) cc_final: 0.8662 (mt) REVERT: a 26 ILE cc_start: 0.9357 (mt) cc_final: 0.9102 (tp) REVERT: a 37 ARG cc_start: 0.7665 (mtm110) cc_final: 0.7438 (mtm-85) REVERT: a 45 TRP cc_start: 0.8683 (t-100) cc_final: 0.8431 (t60) REVERT: q 127 TYR cc_start: 0.9187 (p90) cc_final: 0.8191 (p90) REVERT: r 93 LYS cc_start: 0.8474 (mppt) cc_final: 0.7891 (mmmt) REVERT: r 101 MET cc_start: 0.8218 (mtp) cc_final: 0.7941 (mtp) REVERT: r 109 ASP cc_start: 0.7971 (p0) cc_final: 0.7347 (p0) outliers start: 2 outliers final: 1 residues processed: 865 average time/residue: 0.4677 time to fit residues: 658.6926 Evaluate side-chains 676 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 675 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 161 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 348 optimal weight: 9.9990 chunk 308 optimal weight: 0.8980 chunk 300 optimal weight: 5.9990 chunk 394 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN E 58 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN ** G 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 54 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.079047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.062932 restraints weight = 178930.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.064759 restraints weight = 117565.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.066042 restraints weight = 87049.952| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34578 Z= 0.165 Angle : 0.936 80.546 46909 Z= 0.360 Chirality : 0.045 0.256 5135 Planarity : 0.005 0.061 5952 Dihedral : 7.880 149.057 4761 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.08 % Allowed : 2.18 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 4127 helix: 0.48 (0.12), residues: 1880 sheet: -0.84 (0.28), residues: 330 loop : -0.78 (0.15), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP V 97 HIS 0.008 0.001 HIS X 31 PHE 0.031 0.002 PHE A 56 TYR 0.030 0.002 TYR D 226 ARG 0.011 0.001 ARG R 51 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 1439) hydrogen bonds : angle 5.23239 ( 4155) metal coordination : bond 0.02062 ( 33) metal coordination : angle 15.18181 ( 81) SS BOND : bond 0.00458 ( 3) SS BOND : angle 1.29043 ( 6) covalent geometry : bond 0.00374 (34542) covalent geometry : angle 0.69184 (46822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 840 time to evaluate : 3.592 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: 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: 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: A 1 MET cc_start: 0.7149 (ptm) cc_final: 0.6706 (ppp) REVERT: A 88 MET cc_start: 0.8742 (tpp) cc_final: 0.7486 (tpt) REVERT: B 103 GLU cc_start: 0.9110 (tp30) cc_final: 0.8910 (tp30) REVERT: B 131 MET cc_start: 0.8625 (tpp) cc_final: 0.8364 (tpp) REVERT: B 173 TYR cc_start: 0.8286 (m-80) cc_final: 0.7692 (m-80) REVERT: B 175 TYR cc_start: 0.8916 (p90) cc_final: 0.8556 (p90) REVERT: C 104 ASN cc_start: 0.8685 (m110) cc_final: 0.8435 (m-40) REVERT: C 164 TRP cc_start: 0.8499 (m-10) cc_final: 0.8255 (m-10) REVERT: C 172 MET cc_start: 0.8369 (tpp) cc_final: 0.7901 (tpp) REVERT: C 227 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7756 (tp-100) REVERT: C 229 PHE cc_start: 0.9349 (t80) cc_final: 0.8885 (t80) REVERT: D 145 MET cc_start: 0.8963 (mpp) cc_final: 0.8611 (mpp) REVERT: D 197 MET cc_start: 0.9093 (pmm) cc_final: 0.8890 (pmm) REVERT: D 203 MET cc_start: 0.9290 (mmp) cc_final: 0.8991 (mmp) REVERT: D 210 MET cc_start: 0.9302 (mtm) cc_final: 0.8937 (mtm) REVERT: D 251 PHE cc_start: 0.9062 (t80) cc_final: 0.8722 (t80) REVERT: D 257 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8709 (mt-10) REVERT: D 286 TYR cc_start: 0.8914 (m-80) cc_final: 0.8284 (m-80) REVERT: D 377 SER cc_start: 0.9512 (m) cc_final: 0.9254 (t) REVERT: D 404 LYS cc_start: 0.8974 (mmtp) cc_final: 0.8764 (mmtp) REVERT: D 443 MET cc_start: 0.9201 (mmp) cc_final: 0.8379 (mmp) REVERT: D 456 ILE cc_start: 0.9275 (mm) cc_final: 0.8741 (pt) REVERT: E 109 MET cc_start: 0.7441 (tpt) cc_final: 0.7228 (tpt) REVERT: E 118 TYR cc_start: 0.8188 (m-80) cc_final: 0.7907 (m-80) REVERT: E 242 PHE cc_start: 0.7204 (p90) cc_final: 0.6502 (p90) REVERT: F 62 TRP cc_start: 0.7884 (t60) cc_final: 0.7538 (t60) REVERT: F 136 HIS cc_start: 0.8313 (m-70) cc_final: 0.8016 (m-70) REVERT: F 149 MET cc_start: 0.7411 (mmm) cc_final: 0.6243 (mmm) REVERT: F 262 PHE cc_start: 0.8684 (t80) cc_final: 0.8243 (t80) REVERT: F 422 HIS cc_start: 0.8241 (m-70) cc_final: 0.7849 (m-70) REVERT: G 204 MET cc_start: 0.8263 (mtm) cc_final: 0.8043 (mtp) REVERT: G 218 LEU cc_start: 0.9234 (mt) cc_final: 0.8947 (mt) REVERT: G 263 VAL cc_start: 0.9628 (t) cc_final: 0.9386 (m) REVERT: G 272 ARG cc_start: 0.8490 (ptt180) cc_final: 0.8272 (ptt180) REVERT: G 278 HIS cc_start: 0.8864 (t-90) cc_final: 0.8618 (t-170) REVERT: G 349 GLU cc_start: 0.8642 (pm20) cc_final: 0.8131 (pm20) REVERT: G 354 LEU cc_start: 0.9739 (tp) cc_final: 0.9538 (tt) REVERT: G 473 MET cc_start: 0.8282 (ptm) cc_final: 0.8040 (ttp) REVERT: G 611 THR cc_start: 0.8164 (p) cc_final: 0.7841 (p) REVERT: G 643 ARG cc_start: 0.9002 (mmt90) cc_final: 0.8077 (tmm-80) REVERT: H 17 MET cc_start: 0.9545 (tmm) cc_final: 0.8559 (tmm) REVERT: H 31 MET cc_start: 0.8648 (ttm) cc_final: 0.8408 (ttm) REVERT: H 71 PHE cc_start: 0.7592 (t80) cc_final: 0.7101 (t80) REVERT: H 79 LEU cc_start: 0.9536 (tp) cc_final: 0.9281 (tp) REVERT: H 83 LEU cc_start: 0.9470 (mt) cc_final: 0.9151 (mt) REVERT: H 183 MET cc_start: 0.9305 (mtt) cc_final: 0.8890 (mtt) REVERT: H 185 TRP cc_start: 0.8816 (t-100) cc_final: 0.8322 (t-100) REVERT: H 190 LEU cc_start: 0.9294 (mt) cc_final: 0.9071 (mt) REVERT: H 225 MET cc_start: 0.9239 (mtm) cc_final: 0.8873 (mmt) REVERT: H 234 MET cc_start: 0.9434 (mmm) cc_final: 0.9187 (mmm) REVERT: H 238 THR cc_start: 0.9325 (m) cc_final: 0.8913 (p) REVERT: H 240 ILE cc_start: 0.9525 (mm) cc_final: 0.9321 (mm) REVERT: H 288 LEU cc_start: 0.9467 (mm) cc_final: 0.9187 (mm) REVERT: H 303 TRP cc_start: 0.8704 (t-100) cc_final: 0.8273 (t-100) REVERT: I 48 VAL cc_start: 0.4664 (m) cc_final: 0.4261 (t) REVERT: I 86 TYR cc_start: 0.8638 (t80) cc_final: 0.8433 (t80) REVERT: I 179 THR cc_start: 0.9128 (p) cc_final: 0.8928 (p) REVERT: P 92 MET cc_start: 0.9651 (mmm) cc_final: 0.9357 (mmm) REVERT: P 95 ARG cc_start: 0.9223 (mtp85) cc_final: 0.8945 (mtm-85) REVERT: P 201 ILE cc_start: 0.9151 (mt) cc_final: 0.8941 (tp) REVERT: P 210 GLU cc_start: 0.8292 (tp30) cc_final: 0.7480 (tp30) REVERT: P 233 PHE cc_start: 0.7441 (m-80) cc_final: 0.7120 (m-80) REVERT: P 335 LEU cc_start: 0.8624 (mm) cc_final: 0.8365 (mp) REVERT: P 348 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7334 (mmtm) REVERT: Q 63 THR cc_start: 0.9570 (p) cc_final: 0.9341 (t) REVERT: Q 86 ASN cc_start: 0.8973 (m-40) cc_final: 0.8714 (m-40) REVERT: Q 112 MET cc_start: 0.8408 (mmm) cc_final: 0.7934 (mmm) REVERT: Q 114 TRP cc_start: 0.8919 (m-10) cc_final: 0.8639 (m-10) REVERT: Q 126 LEU cc_start: 0.8897 (tp) cc_final: 0.8668 (tt) REVERT: Q 140 LYS cc_start: 0.9275 (ptpp) cc_final: 0.8897 (ptmm) REVERT: Q 141 ASN cc_start: 0.9241 (m110) cc_final: 0.8589 (m110) REVERT: Q 156 LYS cc_start: 0.8414 (mmpt) cc_final: 0.7972 (mmmt) REVERT: R 51 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7493 (mmm160) REVERT: S 81 ASN cc_start: 0.8765 (t0) cc_final: 0.8456 (t0) REVERT: T 80 LYS cc_start: 0.8753 (tmmt) cc_final: 0.8354 (mptt) REVERT: T 113 LEU cc_start: 0.9154 (mm) cc_final: 0.8765 (mm) REVERT: T 130 ILE cc_start: 0.8250 (mp) cc_final: 0.8018 (mp) REVERT: T 146 ASP cc_start: 0.9297 (m-30) cc_final: 0.9094 (t0) REVERT: W 64 ASP cc_start: 0.9170 (m-30) cc_final: 0.8946 (m-30) REVERT: W 78 ASP cc_start: 0.8934 (t70) cc_final: 0.8632 (t0) REVERT: W 94 GLN cc_start: 0.9246 (mm-40) cc_final: 0.9008 (mm-40) REVERT: W 107 MET cc_start: 0.8841 (mmt) cc_final: 0.8427 (mmm) REVERT: W 127 MET cc_start: 0.7421 (tpp) cc_final: 0.7160 (mmm) REVERT: Z 10 MET cc_start: 0.8649 (mmm) cc_final: 0.7993 (mmt) REVERT: Z 21 TYR cc_start: 0.8294 (p90) cc_final: 0.8078 (p90) REVERT: Z 50 MET cc_start: 0.9324 (ptp) cc_final: 0.9020 (ptp) REVERT: a 9 LEU cc_start: 0.8982 (pp) cc_final: 0.8747 (mm) REVERT: a 12 MET cc_start: 0.9165 (ttm) cc_final: 0.8455 (tpp) REVERT: a 15 CYS cc_start: 0.9282 (m) cc_final: 0.9061 (p) REVERT: a 26 ILE cc_start: 0.9412 (mt) cc_final: 0.9163 (tp) REVERT: a 45 TRP cc_start: 0.8796 (t-100) cc_final: 0.8566 (t-100) REVERT: q 127 TYR cc_start: 0.9119 (p90) cc_final: 0.8204 (p90) REVERT: r 93 LYS cc_start: 0.8474 (mppt) cc_final: 0.7911 (mmmt) REVERT: r 101 MET cc_start: 0.8152 (mtp) cc_final: 0.7941 (mtm) REVERT: r 109 ASP cc_start: 0.8095 (p0) cc_final: 0.7484 (p0) outliers start: 3 outliers final: 1 residues processed: 843 average time/residue: 0.4554 time to fit residues: 617.6370 Evaluate side-chains 660 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 659 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 72 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 317 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 201 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 112 HIS D 131 GLN E 58 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 HIS ** G 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN ** Q 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 67 GLN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 GLN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS q 87 HIS q 91 HIS r 9 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.076919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061933 restraints weight = 182452.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.063613 restraints weight = 117292.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.064620 restraints weight = 86206.997| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.7306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 34578 Z= 0.201 Angle : 0.991 86.832 46909 Z= 0.378 Chirality : 0.046 0.207 5135 Planarity : 0.005 0.059 5952 Dihedral : 7.884 151.798 4761 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.03 % Allowed : 1.82 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 4127 helix: 0.48 (0.12), residues: 1881 sheet: -0.95 (0.28), residues: 334 loop : -0.81 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP V 97 HIS 0.010 0.001 HIS X 31 PHE 0.046 0.002 PHE D 211 TYR 0.022 0.002 TYR D 141 ARG 0.022 0.001 ARG F 152 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 1439) hydrogen bonds : angle 5.34469 ( 4155) metal coordination : bond 0.02894 ( 33) metal coordination : angle 16.26225 ( 81) SS BOND : bond 0.00950 ( 3) SS BOND : angle 2.02590 ( 6) covalent geometry : bond 0.00446 (34542) covalent geometry : angle 0.72506 (46822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 804 time to evaluate : 4.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7332 (ptm) cc_final: 0.6871 (ppp) REVERT: A 86 THR cc_start: 0.8911 (p) cc_final: 0.8631 (p) REVERT: A 88 MET cc_start: 0.8985 (tpp) cc_final: 0.7980 (tpt) REVERT: A 92 PHE cc_start: 0.8160 (m-10) cc_final: 0.7919 (m-10) REVERT: A 98 LEU cc_start: 0.8676 (mm) cc_final: 0.8403 (tp) REVERT: B 114 MET cc_start: 0.9023 (ptt) cc_final: 0.8641 (ptt) REVERT: B 125 PRO cc_start: 0.8953 (Cg_exo) cc_final: 0.8714 (Cg_endo) REVERT: B 131 MET cc_start: 0.8844 (tpp) cc_final: 0.8424 (tpt) REVERT: B 173 TYR cc_start: 0.8406 (m-80) cc_final: 0.8086 (m-80) REVERT: B 175 TYR cc_start: 0.9038 (p90) cc_final: 0.8739 (p90) REVERT: C 104 ASN cc_start: 0.8835 (m110) cc_final: 0.8545 (t0) REVERT: C 166 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8441 (mt-10) REVERT: C 172 MET cc_start: 0.8311 (tpp) cc_final: 0.7765 (tpp) REVERT: C 227 GLN cc_start: 0.8416 (tp40) cc_final: 0.7736 (tp-100) REVERT: C 229 PHE cc_start: 0.9361 (t80) cc_final: 0.8939 (t80) REVERT: C 241 PHE cc_start: 0.7665 (p90) cc_final: 0.7296 (p90) REVERT: D 203 MET cc_start: 0.9278 (mmp) cc_final: 0.8992 (mmp) REVERT: D 222 MET cc_start: 0.8698 (ptm) cc_final: 0.8427 (ptt) REVERT: D 251 PHE cc_start: 0.9116 (t80) cc_final: 0.8890 (t80) REVERT: D 286 TYR cc_start: 0.8916 (m-80) cc_final: 0.8567 (m-80) REVERT: D 377 SER cc_start: 0.9493 (m) cc_final: 0.9227 (t) REVERT: D 443 MET cc_start: 0.9228 (mmp) cc_final: 0.8314 (mmp) REVERT: D 456 ILE cc_start: 0.9227 (mm) cc_final: 0.8782 (pt) REVERT: E 109 MET cc_start: 0.7354 (tpt) cc_final: 0.7099 (tpt) REVERT: E 118 TYR cc_start: 0.8276 (m-80) cc_final: 0.7886 (m-80) REVERT: E 242 PHE cc_start: 0.7288 (p90) cc_final: 0.6643 (p90) REVERT: F 42 PHE cc_start: 0.8679 (t80) cc_final: 0.7687 (t80) REVERT: F 136 HIS cc_start: 0.8325 (m-70) cc_final: 0.7971 (m-70) REVERT: F 149 MET cc_start: 0.7468 (mmm) cc_final: 0.6565 (mmm) REVERT: F 262 PHE cc_start: 0.8745 (t80) cc_final: 0.8505 (t80) REVERT: F 326 LEU cc_start: 0.8034 (pp) cc_final: 0.7831 (pp) REVERT: F 418 GLN cc_start: 0.8830 (mm-40) cc_final: 0.7898 (mt0) REVERT: F 422 HIS cc_start: 0.8442 (m-70) cc_final: 0.7735 (m-70) REVERT: G 77 MET cc_start: 0.9122 (tpt) cc_final: 0.8794 (tpp) REVERT: G 218 LEU cc_start: 0.9272 (mt) cc_final: 0.8999 (mt) REVERT: G 272 ARG cc_start: 0.8603 (ptt180) cc_final: 0.8351 (ptt180) REVERT: G 278 HIS cc_start: 0.9013 (t-90) cc_final: 0.8628 (t-170) REVERT: G 349 GLU cc_start: 0.8603 (pm20) cc_final: 0.8128 (pm20) REVERT: G 626 LEU cc_start: 0.8782 (tp) cc_final: 0.8559 (tp) REVERT: G 643 ARG cc_start: 0.9066 (mmt90) cc_final: 0.8162 (tmm-80) REVERT: G 657 ASP cc_start: 0.7920 (m-30) cc_final: 0.7689 (m-30) REVERT: G 696 MET cc_start: 0.7250 (tmm) cc_final: 0.7017 (tmm) REVERT: H 17 MET cc_start: 0.9568 (tmm) cc_final: 0.8429 (tmm) REVERT: H 71 PHE cc_start: 0.7552 (t80) cc_final: 0.7063 (t80) REVERT: H 83 LEU cc_start: 0.9490 (mt) cc_final: 0.9144 (mt) REVERT: H 165 LEU cc_start: 0.9727 (mp) cc_final: 0.9030 (tp) REVERT: H 185 TRP cc_start: 0.8857 (t-100) cc_final: 0.8618 (t-100) REVERT: H 193 THR cc_start: 0.8893 (p) cc_final: 0.8387 (p) REVERT: H 225 MET cc_start: 0.9188 (mtm) cc_final: 0.8749 (mmt) REVERT: H 234 MET cc_start: 0.9496 (mmm) cc_final: 0.9215 (mmm) REVERT: H 288 LEU cc_start: 0.9572 (mm) cc_final: 0.9188 (mm) REVERT: H 303 TRP cc_start: 0.8786 (t-100) cc_final: 0.8403 (t-100) REVERT: I 48 VAL cc_start: 0.4483 (m) cc_final: 0.4139 (t) REVERT: I 78 PHE cc_start: 0.9087 (m-80) cc_final: 0.8885 (m-80) REVERT: I 90 LYS cc_start: 0.8404 (mmmm) cc_final: 0.8098 (mmmt) REVERT: I 195 ASP cc_start: 0.9026 (m-30) cc_final: 0.8825 (m-30) REVERT: P 89 TYR cc_start: 0.8798 (t80) cc_final: 0.8587 (t80) REVERT: P 92 MET cc_start: 0.9613 (mmm) cc_final: 0.9323 (mmm) REVERT: P 95 ARG cc_start: 0.9258 (mtp85) cc_final: 0.8915 (mtm-85) REVERT: P 201 ILE cc_start: 0.9193 (mt) cc_final: 0.8983 (tp) REVERT: P 233 PHE cc_start: 0.7427 (m-80) cc_final: 0.7120 (m-80) REVERT: P 335 LEU cc_start: 0.8695 (mm) cc_final: 0.8410 (mp) REVERT: P 345 LEU cc_start: 0.8444 (tt) cc_final: 0.8074 (mp) REVERT: P 348 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7331 (mmtm) REVERT: Q 63 THR cc_start: 0.9570 (p) cc_final: 0.9329 (t) REVERT: Q 86 ASN cc_start: 0.9108 (m-40) cc_final: 0.8617 (m-40) REVERT: Q 87 MET cc_start: 0.9257 (mmp) cc_final: 0.8830 (mmp) REVERT: Q 112 MET cc_start: 0.8538 (mmm) cc_final: 0.8198 (mmm) REVERT: Q 114 TRP cc_start: 0.8992 (m-10) cc_final: 0.8744 (m-10) REVERT: Q 126 LEU cc_start: 0.8937 (tp) cc_final: 0.8618 (tt) REVERT: Q 140 LYS cc_start: 0.9249 (ptpp) cc_final: 0.9007 (ptmm) REVERT: Q 156 LYS cc_start: 0.8370 (mmpt) cc_final: 0.7939 (mmmt) REVERT: R 51 ARG cc_start: 0.7973 (mmm160) cc_final: 0.7752 (mmm160) REVERT: R 67 GLN cc_start: 0.4300 (OUTLIER) cc_final: 0.3511 (pp30) REVERT: S 81 ASN cc_start: 0.8834 (t0) cc_final: 0.8540 (t0) REVERT: T 80 LYS cc_start: 0.8734 (tmmt) cc_final: 0.8315 (mptt) REVERT: V 58 MET cc_start: 0.8340 (ttt) cc_final: 0.7467 (tmm) REVERT: W 78 ASP cc_start: 0.9002 (t70) cc_final: 0.8774 (t70) REVERT: W 107 MET cc_start: 0.8906 (mmt) cc_final: 0.8434 (mmm) REVERT: W 127 MET cc_start: 0.7589 (tpp) cc_final: 0.7344 (mmm) REVERT: X 97 PHE cc_start: 0.7861 (m-10) cc_final: 0.7606 (m-10) REVERT: Z 10 MET cc_start: 0.8736 (mmm) cc_final: 0.7805 (mmt) REVERT: Z 21 TYR cc_start: 0.8260 (p90) cc_final: 0.8034 (p90) REVERT: a 12 MET cc_start: 0.9235 (ttm) cc_final: 0.8885 (tpp) REVERT: a 26 ILE cc_start: 0.9467 (mt) cc_final: 0.9248 (tp) REVERT: a 45 TRP cc_start: 0.9005 (t-100) cc_final: 0.8717 (t-100) REVERT: q 9 ARG cc_start: 0.8598 (tpp-160) cc_final: 0.8218 (ttm110) REVERT: q 127 TYR cc_start: 0.9308 (p90) cc_final: 0.8309 (p90) REVERT: r 93 LYS cc_start: 0.8520 (mppt) cc_final: 0.7989 (mmmt) REVERT: r 101 MET cc_start: 0.8345 (mtp) cc_final: 0.7998 (mtm) REVERT: r 109 ASP cc_start: 0.8141 (p0) cc_final: 0.7630 (p0) outliers start: 1 outliers final: 0 residues processed: 805 average time/residue: 0.4608 time to fit residues: 604.1977 Evaluate side-chains 642 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 641 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 179 optimal weight: 0.0000 chunk 338 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 314 optimal weight: 0.8980 chunk 324 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 317 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 406 optimal weight: 7.9990 chunk 393 optimal weight: 20.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 106 HIS ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 ASN ** Q 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 GLN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.078467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.063239 restraints weight = 177673.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.064952 restraints weight = 114836.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.065996 restraints weight = 84926.381| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34578 Z= 0.146 Angle : 0.938 84.290 46909 Z= 0.359 Chirality : 0.045 0.256 5135 Planarity : 0.005 0.058 5952 Dihedral : 7.675 151.609 4761 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.03 % Allowed : 1.10 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 4127 helix: 0.52 (0.12), residues: 1898 sheet: -1.06 (0.27), residues: 355 loop : -0.79 (0.15), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP V 97 HIS 0.005 0.001 HIS F 133 PHE 0.035 0.002 PHE D 200 TYR 0.026 0.002 TYR D 226 ARG 0.015 0.001 ARG F 224 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 1439) hydrogen bonds : angle 5.19775 ( 4155) metal coordination : bond 0.01703 ( 33) metal coordination : angle 15.06429 ( 81) SS BOND : bond 0.00422 ( 3) SS BOND : angle 1.74658 ( 6) covalent geometry : bond 0.00328 (34542) covalent geometry : angle 0.69920 (46822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 841 time to evaluate : 4.256 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: 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: 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: A 1 MET cc_start: 0.7294 (ptm) cc_final: 0.6888 (ppp) REVERT: A 86 THR cc_start: 0.8828 (p) cc_final: 0.8577 (p) REVERT: A 88 MET cc_start: 0.8870 (tpp) cc_final: 0.7836 (tpt) REVERT: A 95 VAL cc_start: 0.8476 (t) cc_final: 0.8147 (t) REVERT: A 98 LEU cc_start: 0.8726 (mm) cc_final: 0.8496 (tp) REVERT: B 129 ASP cc_start: 0.7577 (t0) cc_final: 0.7338 (t0) REVERT: B 131 MET cc_start: 0.8822 (tpp) cc_final: 0.8391 (tpt) REVERT: B 173 TYR cc_start: 0.8364 (m-80) cc_final: 0.8009 (m-80) REVERT: B 175 TYR cc_start: 0.8933 (p90) cc_final: 0.8513 (p90) REVERT: C 104 ASN cc_start: 0.8716 (m110) cc_final: 0.8513 (t0) REVERT: C 118 VAL cc_start: 0.9601 (t) cc_final: 0.9315 (m) REVERT: C 165 TYR cc_start: 0.9251 (m-10) cc_final: 0.9036 (m-10) REVERT: C 172 MET cc_start: 0.8224 (tpp) cc_final: 0.7696 (tpp) REVERT: C 227 GLN cc_start: 0.8365 (tp40) cc_final: 0.7888 (tp-100) REVERT: D 138 ARG cc_start: 0.8866 (mtt90) cc_final: 0.8620 (mpt-90) REVERT: D 197 MET cc_start: 0.9125 (pmm) cc_final: 0.8915 (pmm) REVERT: D 222 MET cc_start: 0.8677 (ptm) cc_final: 0.8427 (ptt) REVERT: D 251 PHE cc_start: 0.9134 (t80) cc_final: 0.8907 (t80) REVERT: D 377 SER cc_start: 0.9482 (m) cc_final: 0.9219 (t) REVERT: D 387 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8717 (tm-30) REVERT: D 404 LYS cc_start: 0.9043 (mmtp) cc_final: 0.8811 (mmtp) REVERT: D 431 HIS cc_start: 0.8767 (m170) cc_final: 0.8512 (m-70) REVERT: D 443 MET cc_start: 0.9237 (mmp) cc_final: 0.8444 (mmp) REVERT: D 456 ILE cc_start: 0.9191 (mm) cc_final: 0.8743 (pt) REVERT: E 118 TYR cc_start: 0.8090 (m-80) cc_final: 0.7857 (m-80) REVERT: E 242 PHE cc_start: 0.7185 (p90) cc_final: 0.6519 (p90) REVERT: F 42 PHE cc_start: 0.8634 (t80) cc_final: 0.7587 (t80) REVERT: F 136 HIS cc_start: 0.8223 (m-70) cc_final: 0.7918 (m-70) REVERT: F 149 MET cc_start: 0.7411 (mmm) cc_final: 0.7107 (mmt) REVERT: F 262 PHE cc_start: 0.8804 (t80) cc_final: 0.8508 (t80) REVERT: F 418 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8019 (tp40) REVERT: F 422 HIS cc_start: 0.8295 (m-70) cc_final: 0.7245 (m90) REVERT: G 77 MET cc_start: 0.9156 (tpt) cc_final: 0.8607 (tpp) REVERT: G 117 MET cc_start: 0.8944 (tpp) cc_final: 0.8642 (tpp) REVERT: G 218 LEU cc_start: 0.9234 (mt) cc_final: 0.8934 (mt) REVERT: G 278 HIS cc_start: 0.8929 (t-90) cc_final: 0.8650 (t-170) REVERT: G 349 GLU cc_start: 0.8601 (pm20) cc_final: 0.8142 (pm20) REVERT: G 387 LEU cc_start: 0.8959 (tp) cc_final: 0.8551 (mt) REVERT: G 579 MET cc_start: 0.8983 (tpt) cc_final: 0.8729 (tpt) REVERT: G 596 TYR cc_start: 0.7122 (m-80) cc_final: 0.6878 (m-10) REVERT: G 643 ARG cc_start: 0.9051 (mmt90) cc_final: 0.8142 (tmm-80) REVERT: H 17 MET cc_start: 0.9591 (tmm) cc_final: 0.8590 (tmm) REVERT: H 71 PHE cc_start: 0.7442 (t80) cc_final: 0.6957 (t80) REVERT: H 83 LEU cc_start: 0.9532 (mt) cc_final: 0.9222 (mt) REVERT: H 118 TRP cc_start: 0.8770 (m100) cc_final: 0.8399 (m100) REVERT: H 133 LEU cc_start: 0.9727 (mt) cc_final: 0.9471 (pp) REVERT: H 183 MET cc_start: 0.9305 (mtt) cc_final: 0.8984 (mtt) REVERT: H 225 MET cc_start: 0.9209 (mtm) cc_final: 0.8642 (mmt) REVERT: H 234 MET cc_start: 0.9479 (mmm) cc_final: 0.9184 (mmm) REVERT: H 238 THR cc_start: 0.9363 (m) cc_final: 0.9032 (p) REVERT: H 303 TRP cc_start: 0.8821 (t-100) cc_final: 0.8379 (t-100) REVERT: I 48 VAL cc_start: 0.4544 (m) cc_final: 0.4206 (t) REVERT: I 90 LYS cc_start: 0.8335 (mmmm) cc_final: 0.8135 (mmmt) REVERT: I 195 ASP cc_start: 0.8997 (m-30) cc_final: 0.8419 (p0) REVERT: P 201 ILE cc_start: 0.9139 (mt) cc_final: 0.8921 (tp) REVERT: P 233 PHE cc_start: 0.7525 (m-80) cc_final: 0.7259 (m-80) REVERT: P 335 LEU cc_start: 0.8781 (mm) cc_final: 0.8513 (mp) REVERT: P 345 LEU cc_start: 0.8576 (tt) cc_final: 0.8104 (mp) REVERT: P 348 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7322 (mmtm) REVERT: Q 63 THR cc_start: 0.9541 (p) cc_final: 0.9266 (t) REVERT: Q 86 ASN cc_start: 0.8849 (m-40) cc_final: 0.8312 (m-40) REVERT: Q 87 MET cc_start: 0.9174 (mmp) cc_final: 0.8656 (mmp) REVERT: Q 112 MET cc_start: 0.8493 (mmm) cc_final: 0.8154 (mmm) REVERT: Q 114 TRP cc_start: 0.8935 (m-10) cc_final: 0.8727 (m-10) REVERT: Q 126 LEU cc_start: 0.8878 (tp) cc_final: 0.8562 (tt) REVERT: Q 156 LYS cc_start: 0.8530 (mmpt) cc_final: 0.7998 (mmmt) REVERT: R 51 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7785 (mmm160) REVERT: S 81 ASN cc_start: 0.8838 (t0) cc_final: 0.8538 (t0) REVERT: T 80 LYS cc_start: 0.8753 (tmmt) cc_final: 0.8372 (mptt) REVERT: V 28 TYR cc_start: 0.8851 (m-80) cc_final: 0.8625 (m-80) REVERT: W 78 ASP cc_start: 0.8971 (t70) cc_final: 0.8739 (t70) REVERT: W 94 GLN cc_start: 0.9291 (mm-40) cc_final: 0.9051 (mm-40) REVERT: W 97 ILE cc_start: 0.9296 (mm) cc_final: 0.9041 (mt) REVERT: W 127 MET cc_start: 0.7632 (tpp) cc_final: 0.7394 (mmm) REVERT: Z 10 MET cc_start: 0.8753 (mmm) cc_final: 0.7919 (mmt) REVERT: Z 21 TYR cc_start: 0.8235 (p90) cc_final: 0.7979 (p90) REVERT: Z 72 MET cc_start: 0.9318 (mmt) cc_final: 0.9076 (mmt) REVERT: a 12 MET cc_start: 0.9185 (ttm) cc_final: 0.8891 (tpp) REVERT: a 26 ILE cc_start: 0.9474 (mt) cc_final: 0.9262 (tp) REVERT: a 45 TRP cc_start: 0.8995 (t-100) cc_final: 0.8713 (t60) REVERT: q 9 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8233 (ttm110) REVERT: q 127 TYR cc_start: 0.9251 (p90) cc_final: 0.8262 (p90) REVERT: r 93 LYS cc_start: 0.8484 (mppt) cc_final: 0.7966 (mmmt) REVERT: r 101 MET cc_start: 0.8435 (mtp) cc_final: 0.8056 (mtm) REVERT: r 109 ASP cc_start: 0.8127 (p0) cc_final: 0.7620 (p0) outliers start: 1 outliers final: 0 residues processed: 842 average time/residue: 0.4532 time to fit residues: 623.6388 Evaluate side-chains 644 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 644 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 271 optimal weight: 6.9990 chunk 394 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 334 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 316 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 131 GLN E 58 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN H 284 GLN I 126 GLN ** Q 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 ASN Q 141 ASN R 67 GLN W 48 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 9 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.077466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.062809 restraints weight = 183513.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.064602 restraints weight = 116140.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.065870 restraints weight = 84266.406| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.7756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34578 Z= 0.167 Angle : 0.952 85.410 46909 Z= 0.367 Chirality : 0.045 0.209 5135 Planarity : 0.006 0.167 5952 Dihedral : 7.559 154.246 4761 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.03 % Allowed : 0.50 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.38 (0.13), residues: 4127 helix: 0.48 (0.12), residues: 1899 sheet: -1.08 (0.27), residues: 344 loop : -0.76 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C 170 HIS 0.008 0.001 HIS H 93 PHE 0.047 0.002 PHE H 224 TYR 0.051 0.002 TYR H 142 ARG 0.019 0.001 ARG X 119 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 1439) hydrogen bonds : angle 5.24319 ( 4155) metal coordination : bond 0.01855 ( 33) metal coordination : angle 15.20927 ( 81) SS BOND : bond 0.00373 ( 3) SS BOND : angle 1.48986 ( 6) covalent geometry : bond 0.00376 (34542) covalent geometry : angle 0.71211 (46822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 810 time to evaluate : 3.751 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: 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: 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: A 1 MET cc_start: 0.7460 (ptm) cc_final: 0.7001 (ppp) REVERT: A 86 THR cc_start: 0.8766 (p) cc_final: 0.8436 (p) REVERT: A 88 MET cc_start: 0.8943 (tpp) cc_final: 0.8146 (tpt) REVERT: A 92 PHE cc_start: 0.8259 (m-10) cc_final: 0.7988 (m-10) REVERT: B 129 ASP cc_start: 0.7953 (t0) cc_final: 0.7676 (t0) REVERT: B 131 MET cc_start: 0.8605 (tpp) cc_final: 0.8329 (tpt) REVERT: B 132 ILE cc_start: 0.8954 (mm) cc_final: 0.8754 (mm) REVERT: B 147 LYS cc_start: 0.9388 (ttpt) cc_final: 0.9178 (ptmt) REVERT: B 173 TYR cc_start: 0.8505 (m-80) cc_final: 0.7991 (m-80) REVERT: B 175 TYR cc_start: 0.8907 (p90) cc_final: 0.8514 (p90) REVERT: C 104 ASN cc_start: 0.8824 (m110) cc_final: 0.8583 (t0) REVERT: C 108 LYS cc_start: 0.8808 (mmtm) cc_final: 0.8564 (mmtt) REVERT: C 166 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8156 (mt-10) REVERT: C 172 MET cc_start: 0.8220 (tpp) cc_final: 0.7533 (tpp) REVERT: C 227 GLN cc_start: 0.8457 (tp40) cc_final: 0.7956 (tp-100) REVERT: C 228 GLU cc_start: 0.8038 (pp20) cc_final: 0.7835 (pp20) REVERT: D 138 ARG cc_start: 0.8807 (mtt90) cc_final: 0.8568 (mpt-90) REVERT: D 190 HIS cc_start: 0.8487 (t70) cc_final: 0.8121 (t-90) REVERT: D 197 MET cc_start: 0.9207 (pmm) cc_final: 0.8839 (pmm) REVERT: D 222 MET cc_start: 0.8767 (ptm) cc_final: 0.8522 (ptt) REVERT: D 292 MET cc_start: 0.8339 (ptp) cc_final: 0.7944 (ptp) REVERT: D 377 SER cc_start: 0.9500 (m) cc_final: 0.9251 (t) REVERT: D 387 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8740 (tm-30) REVERT: D 431 HIS cc_start: 0.8776 (m170) cc_final: 0.8347 (m-70) REVERT: D 443 MET cc_start: 0.9192 (mmp) cc_final: 0.8363 (mmp) REVERT: D 456 ILE cc_start: 0.9198 (mm) cc_final: 0.8811 (pt) REVERT: E 61 ARG cc_start: 0.6495 (mtt180) cc_final: 0.5598 (mmm-85) REVERT: E 118 TYR cc_start: 0.8189 (m-80) cc_final: 0.7936 (m-80) REVERT: E 184 MET cc_start: 0.8992 (ptt) cc_final: 0.8576 (ptt) REVERT: E 242 PHE cc_start: 0.7231 (p90) cc_final: 0.6574 (p90) REVERT: F 136 HIS cc_start: 0.8261 (m-70) cc_final: 0.7878 (m-70) REVERT: F 149 MET cc_start: 0.7326 (mmm) cc_final: 0.6503 (mmm) REVERT: F 226 LYS cc_start: 0.9324 (tppt) cc_final: 0.9114 (mmmt) REVERT: F 262 PHE cc_start: 0.8904 (t80) cc_final: 0.8585 (t80) REVERT: F 326 LEU cc_start: 0.8157 (pp) cc_final: 0.7957 (pp) REVERT: F 418 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8271 (tp40) REVERT: F 422 HIS cc_start: 0.8414 (m-70) cc_final: 0.7890 (m-70) REVERT: G 67 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8504 (tm-30) REVERT: G 77 MET cc_start: 0.9143 (tpt) cc_final: 0.8671 (tpp) REVERT: G 117 MET cc_start: 0.9003 (tpp) cc_final: 0.8646 (tpp) REVERT: G 218 LEU cc_start: 0.9201 (mt) cc_final: 0.8906 (mt) REVERT: G 278 HIS cc_start: 0.8889 (t-90) cc_final: 0.8610 (t-170) REVERT: G 349 GLU cc_start: 0.8574 (pm20) cc_final: 0.8155 (pm20) REVERT: G 579 MET cc_start: 0.9032 (tpt) cc_final: 0.8813 (tpt) REVERT: G 626 LEU cc_start: 0.8668 (tp) cc_final: 0.8449 (tp) REVERT: G 643 ARG cc_start: 0.9046 (mmt90) cc_final: 0.8175 (tmm-80) REVERT: G 657 ASP cc_start: 0.7979 (m-30) cc_final: 0.7731 (m-30) REVERT: G 684 LEU cc_start: 0.8078 (pp) cc_final: 0.7817 (mp) REVERT: G 696 MET cc_start: 0.7680 (tmm) cc_final: 0.7336 (tmm) REVERT: H 17 MET cc_start: 0.9546 (tmm) cc_final: 0.8154 (tmm) REVERT: H 24 GLU cc_start: 0.9420 (tt0) cc_final: 0.9196 (tt0) REVERT: H 31 MET cc_start: 0.8772 (ttm) cc_final: 0.8512 (tpp) REVERT: H 71 PHE cc_start: 0.7545 (t80) cc_final: 0.7150 (t80) REVERT: H 79 LEU cc_start: 0.9551 (tp) cc_final: 0.9329 (tp) REVERT: H 83 LEU cc_start: 0.9518 (mt) cc_final: 0.9218 (mt) REVERT: H 183 MET cc_start: 0.9327 (mtt) cc_final: 0.9014 (mtt) REVERT: H 225 MET cc_start: 0.9138 (mtm) cc_final: 0.8665 (mmt) REVERT: H 234 MET cc_start: 0.9468 (mmm) cc_final: 0.9009 (mmm) REVERT: H 303 TRP cc_start: 0.8812 (t-100) cc_final: 0.8394 (t-100) REVERT: I 48 VAL cc_start: 0.4099 (m) cc_final: 0.3850 (t) REVERT: I 90 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8461 (mmmt) REVERT: I 151 LYS cc_start: 0.9522 (mttm) cc_final: 0.9284 (mmtt) REVERT: I 195 ASP cc_start: 0.8956 (m-30) cc_final: 0.8367 (p0) REVERT: P 201 ILE cc_start: 0.9167 (mt) cc_final: 0.8958 (tp) REVERT: P 233 PHE cc_start: 0.7598 (m-80) cc_final: 0.7356 (m-80) REVERT: P 298 TYR cc_start: 0.7119 (t80) cc_final: 0.6858 (t80) REVERT: P 335 LEU cc_start: 0.8882 (mm) cc_final: 0.8635 (mp) REVERT: P 345 LEU cc_start: 0.8521 (tt) cc_final: 0.8221 (mp) REVERT: P 348 LYS cc_start: 0.7980 (mmtm) cc_final: 0.6816 (mttt) REVERT: Q 63 THR cc_start: 0.9544 (p) cc_final: 0.9262 (t) REVERT: Q 86 ASN cc_start: 0.8900 (m-40) cc_final: 0.8386 (m-40) REVERT: Q 87 MET cc_start: 0.9227 (mmp) cc_final: 0.8696 (mmp) REVERT: Q 101 PHE cc_start: 0.8541 (m-80) cc_final: 0.8021 (m-80) REVERT: Q 112 MET cc_start: 0.8346 (mmm) cc_final: 0.8109 (mmm) REVERT: Q 126 LEU cc_start: 0.8961 (tp) cc_final: 0.8622 (tt) REVERT: Q 140 LYS cc_start: 0.9201 (ptpp) cc_final: 0.8998 (ptmm) REVERT: Q 156 LYS cc_start: 0.8422 (mmpt) cc_final: 0.8042 (mmmt) REVERT: R 51 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7857 (mmm160) REVERT: R 67 GLN cc_start: 0.3982 (OUTLIER) cc_final: 0.3023 (pp30) REVERT: S 81 ASN cc_start: 0.8842 (t0) cc_final: 0.8540 (t0) REVERT: T 80 LYS cc_start: 0.8844 (tmmt) cc_final: 0.8367 (mptt) REVERT: T 122 MET cc_start: 0.8869 (ptm) cc_final: 0.8333 (ppp) REVERT: T 146 ASP cc_start: 0.9384 (t0) cc_final: 0.9149 (t0) REVERT: V 28 TYR cc_start: 0.8933 (m-80) cc_final: 0.8704 (m-80) REVERT: W 94 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8926 (mm110) REVERT: W 127 MET cc_start: 0.7703 (tpp) cc_final: 0.7495 (mmm) REVERT: Z 10 MET cc_start: 0.8841 (mmm) cc_final: 0.8067 (mmt) REVERT: Z 50 MET cc_start: 0.9338 (ptp) cc_final: 0.8929 (ptp) REVERT: a 12 MET cc_start: 0.9229 (ttm) cc_final: 0.8865 (tpp) REVERT: a 26 ILE cc_start: 0.9495 (mt) cc_final: 0.9286 (tp) REVERT: a 38 VAL cc_start: 0.8386 (t) cc_final: 0.8164 (t) REVERT: a 45 TRP cc_start: 0.9050 (t-100) cc_final: 0.8712 (t-100) REVERT: q 9 ARG cc_start: 0.8686 (tpp-160) cc_final: 0.8280 (ttm110) REVERT: q 91 HIS cc_start: 0.7983 (m170) cc_final: 0.7772 (m-70) REVERT: q 127 TYR cc_start: 0.9055 (p90) cc_final: 0.8274 (p90) REVERT: r 93 LYS cc_start: 0.8473 (mppt) cc_final: 0.7974 (mmmt) REVERT: r 101 MET cc_start: 0.8511 (mtp) cc_final: 0.8043 (mtm) REVERT: r 109 ASP cc_start: 0.8201 (p0) cc_final: 0.7750 (p0) REVERT: s 57 LEU cc_start: 0.8602 (mm) cc_final: 0.8053 (pt) outliers start: 1 outliers final: 0 residues processed: 811 average time/residue: 0.4540 time to fit residues: 601.6594 Evaluate side-chains 629 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 628 time to evaluate : 3.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 191 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 226 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 323 optimal weight: 5.9990 chunk 394 optimal weight: 7.9990 chunk 405 optimal weight: 0.6980 chunk 352 optimal weight: 0.7980 chunk 280 optimal weight: 5.9990 chunk 373 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 HIS ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 GLN P 323 HIS ** Q 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.078422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.062995 restraints weight = 181442.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.064831 restraints weight = 117676.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.066100 restraints weight = 86117.921| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.7934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34578 Z= 0.149 Angle : 0.946 83.906 46909 Z= 0.370 Chirality : 0.045 0.233 5135 Planarity : 0.005 0.087 5952 Dihedral : 7.460 153.814 4761 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.43 (0.13), residues: 4127 helix: 0.45 (0.12), residues: 1906 sheet: -1.10 (0.27), residues: 360 loop : -0.80 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 202 HIS 0.010 0.001 HIS X 31 PHE 0.029 0.002 PHE H 224 TYR 0.049 0.002 TYR H 142 ARG 0.014 0.001 ARG X 119 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 1439) hydrogen bonds : angle 5.20190 ( 4155) metal coordination : bond 0.01633 ( 33) metal coordination : angle 14.71774 ( 81) SS BOND : bond 0.00335 ( 3) SS BOND : angle 1.48071 ( 6) covalent geometry : bond 0.00341 (34542) covalent geometry : angle 0.72179 (46822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 815 time to evaluate : 3.692 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: 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: 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: A 1 MET cc_start: 0.7422 (ptm) cc_final: 0.6995 (ppp) REVERT: A 56 PHE cc_start: 0.7521 (m-80) cc_final: 0.7288 (m-80) REVERT: A 87 MET cc_start: 0.5631 (mmt) cc_final: 0.5061 (mmt) REVERT: A 88 MET cc_start: 0.8822 (tpp) cc_final: 0.7954 (tpt) REVERT: B 129 ASP cc_start: 0.7557 (t0) cc_final: 0.7192 (t0) REVERT: B 131 MET cc_start: 0.8740 (tpp) cc_final: 0.8435 (tpt) REVERT: B 147 LYS cc_start: 0.9369 (ttpt) cc_final: 0.9147 (tttt) REVERT: B 173 TYR cc_start: 0.8249 (m-80) cc_final: 0.7947 (m-80) REVERT: B 175 TYR cc_start: 0.8844 (p90) cc_final: 0.8415 (p90) REVERT: C 108 LYS cc_start: 0.8827 (mmtm) cc_final: 0.8572 (mmtt) REVERT: C 118 VAL cc_start: 0.9593 (t) cc_final: 0.9312 (m) REVERT: C 166 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8097 (mt-10) REVERT: C 172 MET cc_start: 0.8013 (tpp) cc_final: 0.7515 (tpp) REVERT: D 138 ARG cc_start: 0.8834 (mtt90) cc_final: 0.8604 (mpt-90) REVERT: D 197 MET cc_start: 0.9149 (pmm) cc_final: 0.8843 (pmm) REVERT: D 222 MET cc_start: 0.8745 (ptm) cc_final: 0.8246 (ptt) REVERT: D 251 PHE cc_start: 0.9143 (t80) cc_final: 0.8858 (t80) REVERT: D 292 MET cc_start: 0.8180 (ptp) cc_final: 0.7881 (ptp) REVERT: D 377 SER cc_start: 0.9499 (m) cc_final: 0.9239 (t) REVERT: D 387 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8731 (tm-30) REVERT: D 431 HIS cc_start: 0.8660 (m170) cc_final: 0.8325 (m-70) REVERT: D 443 MET cc_start: 0.9228 (mmp) cc_final: 0.8421 (mmp) REVERT: D 456 ILE cc_start: 0.9049 (mm) cc_final: 0.8843 (pt) REVERT: E 61 ARG cc_start: 0.6340 (mtt180) cc_final: 0.5434 (mmm-85) REVERT: E 184 MET cc_start: 0.8941 (ptt) cc_final: 0.8484 (ptt) REVERT: E 218 ARG cc_start: 0.7816 (tpm170) cc_final: 0.7488 (mmm-85) REVERT: E 242 PHE cc_start: 0.7203 (p90) cc_final: 0.6566 (p90) REVERT: F 136 HIS cc_start: 0.8236 (m-70) cc_final: 0.7859 (m-70) REVERT: F 149 MET cc_start: 0.7304 (mmm) cc_final: 0.6921 (mmt) REVERT: F 262 PHE cc_start: 0.8929 (t80) cc_final: 0.8574 (t80) REVERT: F 418 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8314 (mt0) REVERT: F 422 HIS cc_start: 0.8377 (m-70) cc_final: 0.8025 (m-70) REVERT: G 67 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8577 (tm-30) REVERT: G 77 MET cc_start: 0.9103 (tpt) cc_final: 0.8649 (tpp) REVERT: G 117 MET cc_start: 0.8984 (tpp) cc_final: 0.8710 (tpp) REVERT: G 218 LEU cc_start: 0.9185 (mt) cc_final: 0.8877 (mt) REVERT: G 250 SER cc_start: 0.8465 (t) cc_final: 0.8249 (t) REVERT: G 278 HIS cc_start: 0.8845 (t-90) cc_final: 0.8623 (t-170) REVERT: G 349 GLU cc_start: 0.8605 (pm20) cc_final: 0.8162 (pm20) REVERT: G 626 LEU cc_start: 0.8659 (tp) cc_final: 0.8437 (tp) REVERT: G 643 ARG cc_start: 0.9042 (mmt90) cc_final: 0.8181 (tmm-80) REVERT: G 657 ASP cc_start: 0.7811 (m-30) cc_final: 0.7578 (m-30) REVERT: H 17 MET cc_start: 0.9550 (tmm) cc_final: 0.8291 (tmm) REVERT: H 71 PHE cc_start: 0.7482 (t80) cc_final: 0.7065 (t80) REVERT: H 79 LEU cc_start: 0.9550 (tp) cc_final: 0.9314 (tp) REVERT: H 83 LEU cc_start: 0.9515 (mt) cc_final: 0.9236 (mt) REVERT: H 133 LEU cc_start: 0.9679 (mt) cc_final: 0.9429 (pp) REVERT: H 225 MET cc_start: 0.9130 (mtm) cc_final: 0.8578 (mmt) REVERT: H 234 MET cc_start: 0.9478 (mmm) cc_final: 0.9074 (mmm) REVERT: H 302 MET cc_start: 0.8716 (mmt) cc_final: 0.8305 (mmt) REVERT: H 303 TRP cc_start: 0.8854 (t-100) cc_final: 0.8339 (t-100) REVERT: I 90 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8194 (mmmt) REVERT: I 195 ASP cc_start: 0.8863 (m-30) cc_final: 0.8292 (p0) REVERT: P 201 ILE cc_start: 0.9169 (mt) cc_final: 0.8965 (tp) REVERT: P 233 PHE cc_start: 0.7698 (m-80) cc_final: 0.7390 (m-80) REVERT: P 298 TYR cc_start: 0.7024 (t80) cc_final: 0.6823 (t80) REVERT: P 335 LEU cc_start: 0.8916 (mm) cc_final: 0.8687 (mp) REVERT: P 345 LEU cc_start: 0.8583 (tt) cc_final: 0.8279 (mp) REVERT: P 348 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7302 (mmtm) REVERT: Q 63 THR cc_start: 0.9553 (p) cc_final: 0.9282 (t) REVERT: Q 87 MET cc_start: 0.9199 (mmp) cc_final: 0.8600 (mmp) REVERT: Q 126 LEU cc_start: 0.8924 (tp) cc_final: 0.8544 (tt) REVERT: Q 156 LYS cc_start: 0.8459 (mmpt) cc_final: 0.8060 (mmmt) REVERT: R 51 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7883 (mmm160) REVERT: S 81 ASN cc_start: 0.8854 (t0) cc_final: 0.8548 (t0) REVERT: T 80 LYS cc_start: 0.8821 (tmmt) cc_final: 0.8424 (mptt) REVERT: T 120 MET cc_start: 0.8540 (mtp) cc_final: 0.8319 (mtt) REVERT: V 28 TYR cc_start: 0.8977 (m-80) cc_final: 0.8751 (m-80) REVERT: W 43 TYR cc_start: 0.8971 (t80) cc_final: 0.8709 (t80) REVERT: W 78 ASP cc_start: 0.9149 (t70) cc_final: 0.8893 (t0) REVERT: W 97 ILE cc_start: 0.9302 (mt) cc_final: 0.8548 (mm) REVERT: Z 10 MET cc_start: 0.8865 (mmm) cc_final: 0.8101 (mmt) REVERT: Z 50 MET cc_start: 0.9246 (ptp) cc_final: 0.8840 (ppp) REVERT: Z 72 MET cc_start: 0.9309 (mmt) cc_final: 0.9095 (mmt) REVERT: a 12 MET cc_start: 0.9180 (ttm) cc_final: 0.8905 (tpp) REVERT: a 15 CYS cc_start: 0.9245 (m) cc_final: 0.8990 (m) REVERT: a 45 TRP cc_start: 0.9116 (t-100) cc_final: 0.8714 (t60) REVERT: a 48 MET cc_start: 0.8876 (mmp) cc_final: 0.8384 (mmm) REVERT: q 9 ARG cc_start: 0.8672 (tpp-160) cc_final: 0.8289 (ttm110) REVERT: q 127 TYR cc_start: 0.9097 (p90) cc_final: 0.8305 (p90) REVERT: r 93 LYS cc_start: 0.8514 (mppt) cc_final: 0.7999 (mmmt) REVERT: r 101 MET cc_start: 0.8527 (mtp) cc_final: 0.8018 (mtm) REVERT: s 57 LEU cc_start: 0.8539 (mm) cc_final: 0.8066 (pt) outliers start: 0 outliers final: 0 residues processed: 815 average time/residue: 0.4540 time to fit residues: 605.7103 Evaluate side-chains 636 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 636 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 332 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 100 optimal weight: 0.0770 chunk 243 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 393 optimal weight: 9.9990 chunk 343 optimal weight: 5.9990 chunk 182 optimal weight: 0.9990 chunk 384 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN E 58 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN H 287 HIS P 71 ASN P 323 HIS ** Q 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 69 HIS q 59 HIS ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 9 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.078424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.063021 restraints weight = 180382.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.064883 restraints weight = 115600.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066205 restraints weight = 83978.926| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.8111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34578 Z= 0.145 Angle : 0.953 83.530 46909 Z= 0.372 Chirality : 0.045 0.225 5135 Planarity : 0.006 0.188 5952 Dihedral : 7.395 154.856 4761 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.42 (0.13), residues: 4127 helix: 0.43 (0.12), residues: 1908 sheet: -0.92 (0.28), residues: 339 loop : -0.81 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP H 185 HIS 0.008 0.001 HIS X 31 PHE 0.049 0.002 PHE b 23 TYR 0.050 0.002 TYR H 142 ARG 0.027 0.001 ARG C 230 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 1439) hydrogen bonds : angle 5.22339 ( 4155) metal coordination : bond 0.01531 ( 33) metal coordination : angle 14.89504 ( 81) SS BOND : bond 0.00308 ( 3) SS BOND : angle 1.46523 ( 6) covalent geometry : bond 0.00333 (34542) covalent geometry : angle 0.72534 (46822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14952.13 seconds wall clock time: 258 minutes 19.23 seconds (15499.23 seconds total)