Starting phenix.real_space_refine on Tue Aug 26 04:26:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xo0_38521/08_2025/8xo0_38521_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xo0_38521/08_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_38521/08_2025/8xo0_38521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xo0_38521/08_2025/8xo0_38521.map" model { file = "/net/cci-nas-00/data/ceres_data/8xo0_38521/08_2025/8xo0_38521_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xo0_38521/08_2025/8xo0_38521_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.27, per 1000 atoms: 0.22 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: 3.07 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.03 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: 6.76 Time building geometry restraints manager: 3.93 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: 12.810 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: 0.040 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 34.090 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.300 ------------------------------------------------------------------------------- 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 : 41.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG D 333 TYR 0.045 0.002 TYR B 112 PHE 0.050 0.002 PHE a 3 TRP 0.036 0.002 TRP G 285 HIS 0.012 0.002 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.01391 (34542) covalent geometry : angle 2.04924 (46822) SS BOND : bond 0.00806 ( 3) SS BOND : angle 2.22935 ( 6) hydrogen bonds : bond 0.23930 ( 1439) hydrogen bonds : angle 8.88220 ( 4155) metal coordination : bond 0.48059 ( 33) metal coordination : angle 16.44467 ( 81) *********************** 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 : 1.265 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: A 10 ASN cc_start: 0.8157 (m-40) cc_final: 0.7327 (t0) REVERT: A 92 PHE cc_start: 0.5106 (m-10) cc_final: 0.4723 (m-10) REVERT: B 106 HIS cc_start: 0.7525 (m-70) cc_final: 0.7311 (m90) REVERT: B 145 LEU cc_start: 0.8512 (tp) cc_final: 0.8302 (tp) REVERT: B 170 TYR cc_start: 0.8066 (t80) cc_final: 0.7619 (t80) REVERT: B 175 TYR cc_start: 0.8031 (p90) cc_final: 0.7820 (p90) REVERT: B 202 LEU cc_start: 0.8438 (tm) cc_final: 0.7734 (tm) REVERT: B 208 LEU cc_start: 0.8973 (tp) cc_final: 0.8768 (tt) REVERT: C 93 ILE cc_start: 0.8059 (mm) cc_final: 0.7347 (mm) REVERT: C 141 ARG cc_start: 0.7639 (ttm170) cc_final: 0.7372 (ttm110) REVERT: C 171 ASP cc_start: 0.7672 (t0) cc_final: 0.7406 (t0) REVERT: D 116 LEU cc_start: 0.8437 (tp) cc_final: 0.8152 (mt) REVERT: D 135 TYR cc_start: 0.8130 (m-80) cc_final: 0.7196 (m-10) REVERT: D 189 THR cc_start: 0.7883 (m) cc_final: 0.7104 (m) REVERT: D 222 MET cc_start: 0.7446 (ptm) cc_final: 0.7227 (ptt) REVERT: D 261 MET cc_start: 0.7565 (mmm) cc_final: 0.7293 (mmm) REVERT: D 278 VAL cc_start: 0.7831 (m) cc_final: 0.7537 (p) REVERT: D 400 ILE cc_start: 0.8747 (pt) cc_final: 0.8546 (pt) REVERT: D 431 HIS cc_start: 0.6582 (m170) cc_final: 0.6053 (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: 0.7945 (mm) REVERT: E 109 MET cc_start: 0.6186 (tpt) cc_final: 0.5828 (mmm) REVERT: E 167 LEU cc_start: 0.8297 (mp) cc_final: 0.7292 (mt) REVERT: F 157 TYR cc_start: 0.6405 (t80) cc_final: 0.5852 (t80) REVERT: F 418 GLN cc_start: 0.7084 (mm-40) cc_final: 0.6612 (mt0) REVERT: G 50 LEU cc_start: 0.8066 (tt) cc_final: 0.7734 (tp) REVERT: G 253 VAL cc_start: 0.7928 (t) cc_final: 0.7666 (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: 0.3987 (tt) REVERT: G 691 ILE cc_start: 0.7267 (tt) cc_final: 0.6109 (tt) REVERT: H 13 ILE cc_start: 0.8886 (mm) cc_final: 0.8646 (mm) REVERT: H 55 LEU cc_start: 0.8332 (mt) cc_final: 0.8077 (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: 0.7450 (p) REVERT: I 77 LEU cc_start: 0.7616 (tt) cc_final: 0.7275 (tt) REVERT: I 153 ILE cc_start: 0.7565 (pp) cc_final: 0.7210 (pp) REVERT: I 177 THR cc_start: 0.8238 (p) cc_final: 0.7433 (p) REVERT: I 190 LEU cc_start: 0.9030 (mt) cc_final: 0.8689 (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: 0.5613 (tpp) REVERT: Q 141 ASN cc_start: 0.6857 (m-40) cc_final: 0.6651 (m110) REVERT: T 110 LEU cc_start: 0.6725 (tp) cc_final: 0.5156 (tp) REVERT: V 55 LYS cc_start: 0.8372 (mmtm) cc_final: 0.7628 (mmtm) REVERT: V 86 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7987 (ttmt) REVERT: W 82 VAL cc_start: 0.9120 (t) cc_final: 0.8796 (p) REVERT: Z 79 LYS cc_start: 0.6986 (ttpt) cc_final: 0.6112 (tptt) REVERT: q 74 PHE cc_start: 0.3379 (t80) cc_final: 0.3090 (t80) outliers start: 10 outliers final: 1 residues processed: 1475 average time/residue: 0.2237 time to fit residues: 511.5518 Evaluate side-chains 827 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 826 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 197 optimal weight: 0.0870 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS 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 D 381 HIS 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 F 393 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN G 388 ASN G 444 HIS G 571 HIS G 604 GLN G 605 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 124 ASN H 169 GLN H 258 ASN ** I 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 154 GLN ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 269 ASN P 356 HIS S 22 HIS T 142 GLN V 21 HIS ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN X 30 HIS ** X 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN X 77 HIS X 109 GLN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 GLN b 71 GLN ** 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: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.086716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.070391 restraints weight = 171366.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.072386 restraints weight = 111040.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.073750 restraints weight = 81214.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.074790 restraints weight = 64954.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.075531 restraints weight = 54991.463| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 34578 Z= 0.201 Angle : 0.995 55.614 46909 Z= 0.437 Chirality : 0.050 0.284 5135 Planarity : 0.007 0.094 5952 Dihedral : 8.362 144.334 4761 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.39 % Allowed : 4.63 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.13), residues: 4127 helix: 0.17 (0.11), residues: 1868 sheet: -1.15 (0.28), residues: 337 loop : -1.36 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 68 TYR 0.049 0.003 TYR B 170 PHE 0.036 0.003 PHE H 223 TRP 0.036 0.002 TRP Q 97 HIS 0.016 0.002 HIS q 91 Details of bonding type rmsd covalent geometry : bond 0.00437 (34542) covalent geometry : angle 0.83075 (46822) SS BOND : bond 0.00426 ( 3) SS BOND : angle 1.59763 ( 6) hydrogen bonds : bond 0.06146 ( 1439) hydrogen bonds : angle 5.83720 ( 4155) metal coordination : bond 0.02178 ( 33) metal coordination : angle 13.21901 ( 81) *********************** 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 1061 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1047 time to evaluate : 1.308 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: A 1 MET cc_start: 0.6526 (ptm) cc_final: 0.6289 (ppp) REVERT: A 10 ASN cc_start: 0.8953 (m-40) cc_final: 0.7554 (t0) REVERT: A 88 MET cc_start: 0.8532 (tpp) cc_final: 0.7833 (ttt) REVERT: B 103 GLU cc_start: 0.9022 (tp30) cc_final: 0.8801 (tp30) REVERT: B 114 MET cc_start: 0.8844 (ptp) cc_final: 0.8467 (ptp) REVERT: B 117 PHE cc_start: 0.9581 (m-80) cc_final: 0.9076 (m-10) REVERT: B 188 ASP cc_start: 0.8562 (t0) cc_final: 0.7295 (t70) REVERT: B 189 ILE cc_start: 0.9396 (mm) cc_final: 0.9131 (mm) REVERT: B 202 LEU cc_start: 0.9540 (tt) cc_final: 0.9291 (tt) REVERT: C 140 ILE cc_start: 0.9061 (tt) cc_final: 0.8860 (pt) REVERT: C 189 ASP cc_start: 0.8198 (t0) cc_final: 0.7669 (t0) REVERT: C 228 GLU cc_start: 0.8230 (pt0) cc_final: 0.7703 (pt0) REVERT: D 94 VAL cc_start: 0.8091 (m) cc_final: 0.7714 (p) REVERT: D 149 GLN cc_start: 0.9343 (tt0) cc_final: 0.9111 (tt0) REVERT: D 185 MET cc_start: 0.9267 (tpp) cc_final: 0.9053 (tpp) REVERT: D 197 MET cc_start: 0.9002 (pmm) cc_final: 0.8631 (pmm) REVERT: D 210 MET cc_start: 0.9267 (mtm) cc_final: 0.8820 (mtm) REVERT: D 222 MET cc_start: 0.8904 (ptm) cc_final: 0.8552 (ptt) REVERT: D 251 PHE cc_start: 0.8998 (t80) cc_final: 0.8508 (t80) REVERT: D 268 TRP cc_start: 0.8589 (t-100) cc_final: 0.8306 (t-100) REVERT: D 286 TYR cc_start: 0.8741 (m-80) cc_final: 0.8412 (m-80) REVERT: D 398 THR cc_start: 0.8085 (p) cc_final: 0.7792 (p) REVERT: D 400 ILE cc_start: 0.9183 (pt) cc_final: 0.8926 (pt) REVERT: D 443 MET cc_start: 0.8883 (mmp) cc_final: 0.8579 (mmp) REVERT: D 456 ILE cc_start: 0.9310 (mm) cc_final: 0.8725 (pt) REVERT: E 87 ARG cc_start: 0.7779 (mmt180) cc_final: 0.7548 (mmt180) REVERT: E 131 ILE cc_start: 0.9046 (mm) cc_final: 0.8819 (mp) REVERT: E 165 ASP cc_start: 0.8484 (t0) cc_final: 0.8219 (t0) REVERT: E 238 LYS cc_start: 0.6892 (mtmt) cc_final: 0.5251 (mmtt) REVERT: F 62 TRP cc_start: 0.7778 (t60) cc_final: 0.7495 (t60) REVERT: F 136 HIS cc_start: 0.8201 (m-70) cc_final: 0.7983 (m-70) REVERT: F 262 PHE cc_start: 0.8027 (t80) cc_final: 0.7444 (t80) REVERT: F 446 LEU cc_start: 0.9509 (tp) cc_final: 0.9277 (tp) REVERT: G 117 MET cc_start: 0.8769 (tpp) cc_final: 0.8410 (tpp) REVERT: G 218 LEU cc_start: 0.9287 (mt) cc_final: 0.9032 (mt) REVERT: G 253 VAL cc_start: 0.9118 (t) cc_final: 0.8903 (t) REVERT: G 387 LEU cc_start: 0.8565 (mt) cc_final: 0.8326 (mt) REVERT: G 526 LEU cc_start: 0.9342 (mt) cc_final: 0.9118 (mt) REVERT: G 626 LEU cc_start: 0.8742 (tp) cc_final: 0.8511 (tp) REVERT: G 639 LEU cc_start: 0.9007 (tt) cc_final: 0.8642 (mp) REVERT: G 657 ASP cc_start: 0.7533 (m-30) cc_final: 0.7284 (m-30) REVERT: H 61 MET cc_start: 0.8191 (ttp) cc_final: 0.7740 (tmm) REVERT: H 83 LEU cc_start: 0.9418 (mt) cc_final: 0.9057 (mt) REVERT: H 146 MET cc_start: 0.8027 (mtt) cc_final: 0.7816 (mtt) REVERT: H 179 TRP cc_start: 0.9219 (p-90) cc_final: 0.8852 (p-90) REVERT: H 183 MET cc_start: 0.8997 (mtm) cc_final: 0.8752 (mtt) REVERT: H 225 MET cc_start: 0.9444 (mtm) cc_final: 0.9212 (mmm) REVERT: H 240 ILE cc_start: 0.9422 (mm) cc_final: 0.8904 (mm) REVERT: H 284 GLN cc_start: 0.9447 (mm110) cc_final: 0.8823 (mm-40) REVERT: H 288 LEU cc_start: 0.9563 (mm) cc_final: 0.9201 (mm) REVERT: P 48 ARG cc_start: 0.6289 (tpp80) cc_final: 0.6071 (tpp80) REVERT: P 233 PHE cc_start: 0.7313 (m-80) cc_final: 0.7052 (m-80) REVERT: P 328 MET cc_start: 0.7102 (pmm) cc_final: 0.6475 (pmm) REVERT: P 335 LEU cc_start: 0.8227 (mt) cc_final: 0.7986 (tp) REVERT: P 348 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7633 (mmtt) REVERT: Q 87 MET cc_start: 0.9082 (mmp) cc_final: 0.8857 (mmm) REVERT: Q 112 MET cc_start: 0.7882 (mmm) cc_final: 0.7351 (mmm) REVERT: Q 121 LEU cc_start: 0.9428 (mm) cc_final: 0.9206 (mm) REVERT: Q 137 PHE cc_start: 0.8825 (t80) cc_final: 0.7447 (t80) REVERT: S 81 ASN cc_start: 0.8616 (t0) cc_final: 0.8339 (t0) REVERT: T 113 LEU cc_start: 0.9085 (mm) cc_final: 0.8454 (mm) REVERT: V 34 ILE cc_start: 0.9022 (mt) cc_final: 0.8590 (tp) REVERT: W 78 ASP cc_start: 0.8860 (t70) cc_final: 0.8583 (t70) REVERT: W 105 HIS cc_start: 0.8485 (m90) cc_final: 0.7964 (m90) REVERT: X 32 TYR cc_start: 0.7808 (t80) cc_final: 0.7216 (t80) REVERT: X 97 PHE cc_start: 0.8265 (m-80) cc_final: 0.8064 (m-10) REVERT: Z 10 MET cc_start: 0.7336 (mtp) cc_final: 0.7106 (mtp) REVERT: Z 51 MET cc_start: 0.8923 (tmm) cc_final: 0.8623 (tmm) REVERT: a 4 GLU cc_start: 0.7715 (mp0) cc_final: 0.7503 (mp0) REVERT: a 9 LEU cc_start: 0.8788 (pp) cc_final: 0.8243 (mt) REVERT: a 15 CYS cc_start: 0.9229 (m) cc_final: 0.8916 (m) REVERT: r 93 LYS cc_start: 0.8412 (mppt) cc_final: 0.7731 (mmmt) REVERT: s 42 THR cc_start: 0.7456 (p) cc_final: 0.7083 (p) REVERT: s 52 LEU cc_start: 0.7497 (mt) cc_final: 0.7283 (mt) outliers start: 14 outliers final: 3 residues processed: 1055 average time/residue: 0.2073 time to fit residues: 351.2415 Evaluate side-chains 747 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 744 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 115 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 372 optimal weight: 0.7980 chunk 362 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 166 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 112 HIS D 131 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 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 142 GLN G 495 ASN G 652 ASN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 95 GLN X 124 GLN ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 31 ASN ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.085309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.068600 restraints weight = 174746.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.070707 restraints weight = 114053.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.072135 restraints weight = 82448.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.073202 restraints weight = 65746.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.073927 restraints weight = 55448.860| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5384 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= 0.184 Angle : 0.911 53.925 46909 Z= 0.385 Chirality : 0.046 0.256 5135 Planarity : 0.006 0.077 5952 Dihedral : 8.145 141.038 4761 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.22 % Allowed : 3.64 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.13), residues: 4127 helix: 0.39 (0.12), residues: 1876 sheet: -1.16 (0.26), residues: 357 loop : -1.09 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 299 TYR 0.055 0.002 TYR H 282 PHE 0.042 0.003 PHE B 121 TRP 0.042 0.002 TRP G 510 HIS 0.017 0.002 HIS F 422 Details of bonding type rmsd covalent geometry : bond 0.00394 (34542) covalent geometry : angle 0.72947 (46822) SS BOND : bond 0.00495 ( 3) SS BOND : angle 1.50352 ( 6) hydrogen bonds : bond 0.05170 ( 1439) hydrogen bonds : angle 5.47376 ( 4155) metal coordination : bond 0.01926 ( 33) metal coordination : angle 13.16354 ( 81) *********************** 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 939 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 931 time to evaluate : 1.339 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 10 ASN cc_start: 0.8946 (m-40) cc_final: 0.7771 (t0) REVERT: A 88 MET cc_start: 0.8391 (tpp) cc_final: 0.7453 (ttt) REVERT: A 99 SER cc_start: 0.8264 (t) cc_final: 0.8023 (p) REVERT: B 104 MET cc_start: 0.9116 (tmm) cc_final: 0.8684 (tmm) REVERT: B 117 PHE cc_start: 0.9546 (m-80) cc_final: 0.9044 (m-10) REVERT: B 173 TYR cc_start: 0.7456 (m-80) cc_final: 0.7061 (m-80) REVERT: B 202 LEU cc_start: 0.9516 (tt) cc_final: 0.9297 (tt) REVERT: C 189 ASP cc_start: 0.8185 (t0) cc_final: 0.7602 (t0) REVERT: C 203 LEU cc_start: 0.9461 (pt) cc_final: 0.9147 (pp) REVERT: C 227 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8033 (tm-30) REVERT: C 228 GLU cc_start: 0.8246 (pt0) cc_final: 0.7688 (pt0) REVERT: D 136 PHE cc_start: 0.8914 (m-80) cc_final: 0.8562 (m-80) REVERT: D 145 MET cc_start: 0.8605 (mtt) cc_final: 0.8389 (mtm) REVERT: D 148 GLU cc_start: 0.8270 (pt0) cc_final: 0.8036 (pt0) REVERT: D 185 MET cc_start: 0.9372 (tpp) cc_final: 0.9164 (tpp) REVERT: D 197 MET cc_start: 0.9027 (pmm) cc_final: 0.8778 (pmm) REVERT: D 203 MET cc_start: 0.9388 (mmp) cc_final: 0.9139 (mmp) REVERT: D 214 TYR cc_start: 0.8541 (m-10) cc_final: 0.8324 (m-10) REVERT: D 222 MET cc_start: 0.8789 (ptm) cc_final: 0.8067 (ppp) REVERT: D 251 PHE cc_start: 0.9041 (t80) cc_final: 0.8504 (t80) REVERT: D 257 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8532 (mt-10) REVERT: D 268 TRP cc_start: 0.8715 (t-100) cc_final: 0.8500 (t-100) REVERT: D 286 TYR cc_start: 0.8756 (m-80) cc_final: 0.7927 (m-80) REVERT: D 443 MET cc_start: 0.9047 (mmp) cc_final: 0.8618 (mmp) REVERT: D 456 ILE cc_start: 0.9278 (mm) cc_final: 0.8582 (pt) REVERT: E 87 ARG cc_start: 0.7900 (mmt180) cc_final: 0.7668 (mmt180) REVERT: F 62 TRP cc_start: 0.7925 (t60) cc_final: 0.7707 (t60) REVERT: F 262 PHE cc_start: 0.8087 (t80) cc_final: 0.7372 (t80) REVERT: F 292 MET cc_start: 0.7148 (mtm) cc_final: 0.6778 (mtt) REVERT: G 39 GLN cc_start: 0.8702 (tp40) cc_final: 0.8149 (tm-30) REVERT: G 117 MET cc_start: 0.8744 (tpp) cc_final: 0.8544 (tpp) REVERT: G 218 LEU cc_start: 0.9243 (mt) cc_final: 0.8997 (mt) REVERT: G 278 HIS cc_start: 0.8697 (t-90) cc_final: 0.8246 (t-90) REVERT: G 387 LEU cc_start: 0.8671 (mt) cc_final: 0.8427 (mt) REVERT: G 526 LEU cc_start: 0.9387 (mt) cc_final: 0.9187 (mt) REVERT: G 646 LEU cc_start: 0.9515 (mt) cc_final: 0.9295 (mt) REVERT: H 24 GLU cc_start: 0.9296 (tt0) cc_final: 0.8837 (tt0) REVERT: H 31 MET cc_start: 0.8670 (ttm) cc_final: 0.8391 (mmm) REVERT: H 53 MET cc_start: 0.8865 (mmp) cc_final: 0.8462 (ttt) REVERT: H 61 MET cc_start: 0.8019 (ttp) cc_final: 0.7769 (tmm) REVERT: H 83 LEU cc_start: 0.9446 (mt) cc_final: 0.9040 (mt) REVERT: H 84 SER cc_start: 0.9576 (m) cc_final: 0.9326 (p) REVERT: H 157 ASN cc_start: 0.8268 (t0) cc_final: 0.8007 (t0) REVERT: H 181 MET cc_start: 0.8528 (mtm) cc_final: 0.8313 (mtm) REVERT: H 238 THR cc_start: 0.9156 (m) cc_final: 0.8926 (p) REVERT: H 281 ARG cc_start: 0.8517 (ptp-170) cc_final: 0.8006 (ptp-170) REVERT: H 284 GLN cc_start: 0.9518 (mm110) cc_final: 0.8959 (mm-40) REVERT: H 288 LEU cc_start: 0.9578 (mm) cc_final: 0.9310 (mm) REVERT: I 48 VAL cc_start: 0.4539 (m) cc_final: 0.4140 (t) REVERT: I 73 THR cc_start: 0.9516 (p) cc_final: 0.9116 (p) REVERT: I 195 ASP cc_start: 0.8928 (m-30) cc_final: 0.8699 (m-30) REVERT: P 92 MET cc_start: 0.9557 (mmm) cc_final: 0.8765 (mmt) REVERT: P 95 ARG cc_start: 0.9162 (mtp180) cc_final: 0.8740 (mtm-85) REVERT: P 97 MET cc_start: 0.8714 (ptm) cc_final: 0.8505 (ptm) REVERT: P 233 PHE cc_start: 0.7265 (m-80) cc_final: 0.6957 (m-80) REVERT: P 328 MET cc_start: 0.7130 (pmm) cc_final: 0.6535 (pmm) REVERT: P 335 LEU cc_start: 0.8334 (mt) cc_final: 0.8094 (tp) REVERT: P 348 LYS cc_start: 0.8072 (mmtm) cc_final: 0.6840 (ttmt) REVERT: Q 71 HIS cc_start: 0.8960 (m90) cc_final: 0.8629 (m-70) REVERT: Q 78 ARG cc_start: 0.8463 (ptm160) cc_final: 0.8189 (ptm160) REVERT: Q 101 PHE cc_start: 0.8463 (m-80) cc_final: 0.8011 (m-80) REVERT: Q 112 MET cc_start: 0.7812 (mmm) cc_final: 0.7561 (mmm) REVERT: Q 141 ASN cc_start: 0.9203 (m110) cc_final: 0.8672 (m110) REVERT: Q 156 LYS cc_start: 0.8178 (mmpt) cc_final: 0.7918 (mmmt) REVERT: T 113 LEU cc_start: 0.9133 (mm) cc_final: 0.8713 (mm) REVERT: T 140 CYS cc_start: 0.3680 (OUTLIER) cc_final: 0.2823 (m) REVERT: V 93 LYS cc_start: 0.9393 (mtmm) cc_final: 0.9026 (mttt) REVERT: W 71 MET cc_start: 0.8658 (mmm) cc_final: 0.8294 (mmm) REVERT: W 78 ASP cc_start: 0.8897 (t70) cc_final: 0.8603 (t70) REVERT: W 85 LEU cc_start: 0.9474 (mt) cc_final: 0.9263 (mt) REVERT: W 95 GLU cc_start: 0.8225 (tp30) cc_final: 0.7884 (tp30) REVERT: W 105 HIS cc_start: 0.8501 (m90) cc_final: 0.8064 (m90) REVERT: W 127 MET cc_start: 0.6983 (tpp) cc_final: 0.6605 (mmm) REVERT: X 32 TYR cc_start: 0.7800 (t80) cc_final: 0.6797 (t80) REVERT: X 71 PHE cc_start: 0.8163 (m-10) cc_final: 0.7669 (m-80) REVERT: X 83 THR cc_start: 0.9158 (m) cc_final: 0.8705 (m) REVERT: Z 10 MET cc_start: 0.7750 (mmm) cc_final: 0.6965 (mmt) REVERT: Z 21 TYR cc_start: 0.8053 (p90) cc_final: 0.7775 (p90) REVERT: a 9 LEU cc_start: 0.8787 (pp) cc_final: 0.8440 (mp) REVERT: a 11 ILE cc_start: 0.8271 (mm) cc_final: 0.7735 (mm) REVERT: a 15 CYS cc_start: 0.9259 (m) cc_final: 0.8830 (m) REVERT: a 26 ILE cc_start: 0.9206 (mt) cc_final: 0.8850 (tp) REVERT: q 127 TYR cc_start: 0.8749 (p90) cc_final: 0.8496 (p90) REVERT: r 93 LYS cc_start: 0.8343 (mppt) cc_final: 0.7623 (mmmt) REVERT: s 42 THR cc_start: 0.7418 (p) cc_final: 0.7025 (p) outliers start: 8 outliers final: 3 residues processed: 936 average time/residue: 0.1912 time to fit residues: 290.4518 Evaluate side-chains 685 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 681 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 403 optimal weight: 5.9990 chunk 100 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 353 optimal weight: 3.9990 chunk 376 optimal weight: 6.9990 chunk 267 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 279 optimal weight: 7.9990 chunk 379 optimal weight: 2.9990 chunk 345 optimal weight: 6.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 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 ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN F 303 HIS ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 460 HIS H 258 ASN I 193 ASN I 204 ASN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN P 166 HIS P 341 GLN Q 93 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 103 GLN ** X 124 GLN ** 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** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.080741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.064913 restraints weight = 177809.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.066768 restraints weight = 116724.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.068038 restraints weight = 86521.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.068725 restraints weight = 69806.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.069459 restraints weight = 61332.928| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 34578 Z= 0.215 Angle : 0.992 72.709 46909 Z= 0.384 Chirality : 0.046 0.237 5135 Planarity : 0.006 0.066 5952 Dihedral : 8.077 143.263 4761 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.13), residues: 4127 helix: 0.37 (0.12), residues: 1885 sheet: -0.88 (0.28), residues: 335 loop : -0.93 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 152 TYR 0.040 0.002 TYR I 38 PHE 0.037 0.003 PHE H 130 TRP 0.034 0.002 TRP V 97 HIS 0.016 0.002 HIS F 422 Details of bonding type rmsd covalent geometry : bond 0.00479 (34542) covalent geometry : angle 0.73173 (46822) SS BOND : bond 0.01704 ( 3) SS BOND : angle 1.63344 ( 6) hydrogen bonds : bond 0.04644 ( 1439) hydrogen bonds : angle 5.40595 ( 4155) metal coordination : bond 0.02730 ( 33) metal coordination : angle 16.12772 ( 81) *********************** 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 861 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 858 time to evaluate : 0.915 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: A 88 MET cc_start: 0.8610 (tpp) cc_final: 0.8001 (ttt) REVERT: A 99 SER cc_start: 0.8413 (t) cc_final: 0.8169 (p) REVERT: B 86 ARG cc_start: 0.8645 (mtt90) cc_final: 0.8228 (mtt90) REVERT: B 104 MET cc_start: 0.9072 (tmm) cc_final: 0.8634 (tmm) REVERT: B 114 MET cc_start: 0.9051 (ptp) cc_final: 0.8436 (ptt) REVERT: B 117 PHE cc_start: 0.9593 (m-80) cc_final: 0.9146 (m-10) REVERT: B 173 TYR cc_start: 0.7968 (m-80) cc_final: 0.7160 (m-80) REVERT: B 190 TYR cc_start: 0.7838 (m-80) cc_final: 0.7489 (m-80) REVERT: C 227 GLN cc_start: 0.8393 (tm-30) cc_final: 0.6658 (tm-30) REVERT: D 185 MET cc_start: 0.9346 (tpp) cc_final: 0.9068 (tpp) REVERT: D 197 MET cc_start: 0.9140 (pmm) cc_final: 0.8831 (pmm) REVERT: D 203 MET cc_start: 0.9463 (mmp) cc_final: 0.9207 (mmp) REVERT: D 210 MET cc_start: 0.9207 (mtm) cc_final: 0.8983 (mtm) REVERT: D 257 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8720 (mt-10) REVERT: D 268 TRP cc_start: 0.8838 (t-100) cc_final: 0.8545 (t-100) REVERT: D 443 MET cc_start: 0.9067 (mmp) cc_final: 0.8552 (mmp) REVERT: D 456 ILE cc_start: 0.9300 (mm) cc_final: 0.8707 (pt) REVERT: E 118 TYR cc_start: 0.8400 (m-80) cc_final: 0.8069 (m-80) REVERT: E 140 MET cc_start: 0.9247 (ptp) cc_final: 0.9006 (ptp) REVERT: E 184 MET cc_start: 0.8656 (ptt) cc_final: 0.8431 (ptt) REVERT: E 242 PHE cc_start: 0.7227 (p90) cc_final: 0.6578 (p90) REVERT: F 62 TRP cc_start: 0.7936 (t60) cc_final: 0.7694 (t60) REVERT: F 136 HIS cc_start: 0.8288 (m-70) cc_final: 0.8044 (m-70) REVERT: F 149 MET cc_start: 0.7061 (mmm) cc_final: 0.5748 (mmm) REVERT: F 262 PHE cc_start: 0.8348 (t80) cc_final: 0.8089 (t80) REVERT: F 292 MET cc_start: 0.7297 (mtm) cc_final: 0.7046 (mtt) REVERT: F 422 HIS cc_start: 0.8365 (m-70) cc_final: 0.8062 (m-70) REVERT: G 39 GLN cc_start: 0.8858 (tp40) cc_final: 0.8229 (tm-30) REVERT: G 77 MET cc_start: 0.9047 (tpt) cc_final: 0.8810 (tpp) REVERT: G 213 MET cc_start: 0.8340 (ttp) cc_final: 0.8073 (tmm) REVERT: G 218 LEU cc_start: 0.9297 (mt) cc_final: 0.9066 (mt) REVERT: G 272 ARG cc_start: 0.8548 (ptt180) cc_final: 0.8285 (ptt180) REVERT: G 278 HIS cc_start: 0.8930 (t-90) cc_final: 0.8585 (t-170) REVERT: G 333 PHE cc_start: 0.8196 (m-80) cc_final: 0.7896 (m-10) REVERT: G 349 GLU cc_start: 0.8565 (pm20) cc_final: 0.8132 (pm20) REVERT: G 387 LEU cc_start: 0.8780 (mt) cc_final: 0.8565 (mt) REVERT: G 473 MET cc_start: 0.8209 (ptm) cc_final: 0.7861 (ttp) REVERT: G 626 LEU cc_start: 0.8763 (tp) cc_final: 0.8552 (tp) REVERT: G 643 ARG cc_start: 0.8981 (mmt90) cc_final: 0.8018 (tmm-80) REVERT: H 61 MET cc_start: 0.8308 (ttp) cc_final: 0.8043 (tmm) REVERT: H 79 LEU cc_start: 0.9547 (tp) cc_final: 0.9322 (tp) REVERT: H 83 LEU cc_start: 0.9474 (mt) cc_final: 0.9154 (mt) REVERT: H 183 MET cc_start: 0.9216 (mtt) cc_final: 0.8513 (mtt) REVERT: H 192 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8545 (tm-30) REVERT: H 240 ILE cc_start: 0.9410 (mm) cc_final: 0.9167 (mm) REVERT: I 48 VAL cc_start: 0.4312 (m) cc_final: 0.3989 (t) REVERT: I 195 ASP cc_start: 0.9000 (m-30) cc_final: 0.8738 (m-30) REVERT: P 48 ARG cc_start: 0.6248 (tpp80) cc_final: 0.6004 (tpp80) REVERT: P 76 MET cc_start: 0.8698 (ppp) cc_final: 0.8257 (ppp) REVERT: P 233 PHE cc_start: 0.7208 (m-80) cc_final: 0.6886 (m-80) REVERT: P 328 MET cc_start: 0.7386 (pmm) cc_final: 0.6867 (pmm) REVERT: P 335 LEU cc_start: 0.8363 (mt) cc_final: 0.8088 (tp) REVERT: P 348 LYS cc_start: 0.8052 (mmtm) cc_final: 0.6797 (mttp) REVERT: Q 78 ARG cc_start: 0.8640 (ptm160) cc_final: 0.8398 (ptm160) REVERT: Q 106 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.7990 (mmm160) REVERT: Q 112 MET cc_start: 0.8324 (mmm) cc_final: 0.7656 (mmm) REVERT: Q 117 THR cc_start: 0.8411 (t) cc_final: 0.8010 (t) REVERT: Q 126 LEU cc_start: 0.8940 (tp) cc_final: 0.8691 (tt) REVERT: Q 141 ASN cc_start: 0.9291 (m110) cc_final: 0.8633 (m110) REVERT: Q 156 LYS cc_start: 0.8225 (mmpt) cc_final: 0.7977 (mmmt) REVERT: S 20 ARG cc_start: 0.7783 (mtm180) cc_final: 0.7552 (mtm180) REVERT: T 113 LEU cc_start: 0.9168 (mm) cc_final: 0.8778 (mm) REVERT: V 79 GLU cc_start: 0.8910 (mp0) cc_final: 0.8709 (mp0) REVERT: V 93 LYS cc_start: 0.9345 (mtmm) cc_final: 0.9004 (mttt) REVERT: W 71 MET cc_start: 0.8759 (mmm) cc_final: 0.8308 (mmm) REVERT: W 78 ASP cc_start: 0.8916 (t70) cc_final: 0.8641 (t70) REVERT: W 85 LEU cc_start: 0.9474 (mt) cc_final: 0.9261 (mt) REVERT: W 94 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8891 (mm-40) REVERT: W 95 GLU cc_start: 0.8342 (tp30) cc_final: 0.8056 (tp30) REVERT: W 127 MET cc_start: 0.7172 (tpp) cc_final: 0.6861 (mmm) REVERT: X 71 PHE cc_start: 0.8140 (m-10) cc_final: 0.7632 (m-80) REVERT: Z 10 MET cc_start: 0.8204 (mmm) cc_final: 0.7682 (mmt) REVERT: Z 21 TYR cc_start: 0.8129 (p90) cc_final: 0.7920 (p90) REVERT: Z 50 MET cc_start: 0.9402 (ptp) cc_final: 0.9198 (ptp) REVERT: Z 105 LYS cc_start: 0.7766 (mptt) cc_final: 0.7505 (tppt) REVERT: a 9 LEU cc_start: 0.8815 (pp) cc_final: 0.8488 (mt) REVERT: a 26 ILE cc_start: 0.9313 (mt) cc_final: 0.9018 (tp) REVERT: q 91 HIS cc_start: 0.8426 (m-70) cc_final: 0.8133 (m90) REVERT: q 127 TYR cc_start: 0.8932 (p90) cc_final: 0.7947 (p90) REVERT: r 93 LYS cc_start: 0.8477 (mppt) cc_final: 0.7798 (mmmt) outliers start: 3 outliers final: 0 residues processed: 861 average time/residue: 0.1830 time to fit residues: 258.3101 Evaluate side-chains 657 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 657 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 176 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 309 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 267 optimal weight: 20.0000 chunk 294 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 chunk 268 optimal weight: 0.8980 chunk 273 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 166 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 131 GLN D 149 GLN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 132 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 G 74 ASN G 123 ASN G 498 GLN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN I 204 ASN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 HIS ** X 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.081461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.065515 restraints weight = 178695.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.067450 restraints weight = 116645.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.068792 restraints weight = 85425.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.069782 restraints weight = 68379.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.070440 restraints weight = 57898.277| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34578 Z= 0.159 Angle : 0.946 73.528 46909 Z= 0.358 Chirality : 0.045 0.221 5135 Planarity : 0.005 0.062 5952 Dihedral : 7.816 144.901 4761 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.13), residues: 4127 helix: 0.48 (0.12), residues: 1883 sheet: -0.79 (0.28), residues: 350 loop : -0.88 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 224 TYR 0.031 0.002 TYR F 46 PHE 0.026 0.002 PHE H 280 TRP 0.041 0.002 TRP V 97 HIS 0.011 0.001 HIS F 422 Details of bonding type rmsd covalent geometry : bond 0.00358 (34542) covalent geometry : angle 0.68844 (46822) SS BOND : bond 0.00495 ( 3) SS BOND : angle 1.46131 ( 6) hydrogen bonds : bond 0.04376 ( 1439) hydrogen bonds : angle 5.22641 ( 4155) metal coordination : bond 0.02096 ( 33) metal coordination : angle 15.64048 ( 81) *********************** 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 876 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 874 time to evaluate : 0.831 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: A 87 MET cc_start: 0.7973 (mmp) cc_final: 0.7660 (mmt) REVERT: A 88 MET cc_start: 0.8816 (tpp) cc_final: 0.8253 (ttt) REVERT: B 86 ARG cc_start: 0.8749 (mtt90) cc_final: 0.8342 (mtt90) REVERT: B 104 MET cc_start: 0.9018 (tmm) cc_final: 0.8595 (tmm) REVERT: B 114 MET cc_start: 0.9188 (ptp) cc_final: 0.8465 (ptt) REVERT: B 117 PHE cc_start: 0.9603 (m-80) cc_final: 0.9165 (m-10) REVERT: B 131 MET cc_start: 0.8788 (tpp) cc_final: 0.8509 (tpt) REVERT: B 170 TYR cc_start: 0.8806 (t80) cc_final: 0.8595 (t80) REVERT: C 172 MET cc_start: 0.8501 (tpp) cc_final: 0.7335 (tpp) REVERT: C 241 PHE cc_start: 0.7232 (p90) cc_final: 0.6916 (p90) REVERT: D 126 TYR cc_start: 0.8672 (m-10) cc_final: 0.8264 (m-10) REVERT: D 185 MET cc_start: 0.9314 (tpp) cc_final: 0.9044 (tpp) REVERT: D 190 HIS cc_start: 0.8554 (t-170) cc_final: 0.8328 (t70) REVERT: D 197 MET cc_start: 0.9152 (pmm) cc_final: 0.8952 (pmm) REVERT: D 210 MET cc_start: 0.9195 (mtm) cc_final: 0.8895 (mtm) REVERT: D 214 TYR cc_start: 0.8513 (m-10) cc_final: 0.8312 (m-10) REVERT: D 222 MET cc_start: 0.9054 (ptt) cc_final: 0.8841 (ptt) REVERT: D 251 PHE cc_start: 0.9064 (t80) cc_final: 0.8673 (t80) REVERT: D 268 TRP cc_start: 0.8853 (t-100) cc_final: 0.8581 (t-100) REVERT: D 286 TYR cc_start: 0.8569 (m-80) cc_final: 0.8341 (m-80) REVERT: D 377 SER cc_start: 0.9452 (m) cc_final: 0.9226 (t) REVERT: D 443 MET cc_start: 0.9043 (mmp) cc_final: 0.8536 (mmp) REVERT: D 456 ILE cc_start: 0.9253 (mm) cc_final: 0.8657 (pt) REVERT: E 118 TYR cc_start: 0.8146 (m-80) cc_final: 0.7826 (m-80) REVERT: E 141 LEU cc_start: 0.9056 (mt) cc_final: 0.8821 (mt) REVERT: E 242 PHE cc_start: 0.7158 (p90) cc_final: 0.6467 (p90) REVERT: F 62 TRP cc_start: 0.7891 (t60) cc_final: 0.7644 (t60) REVERT: F 136 HIS cc_start: 0.8269 (m-70) cc_final: 0.8015 (m-70) REVERT: F 149 MET cc_start: 0.7044 (mmm) cc_final: 0.6031 (mmm) REVERT: F 292 MET cc_start: 0.7173 (mtm) cc_final: 0.6933 (mtt) REVERT: G 39 GLN cc_start: 0.8870 (tp40) cc_final: 0.8254 (tm-30) REVERT: G 66 HIS cc_start: 0.8290 (t-90) cc_final: 0.7762 (t70) REVERT: G 77 MET cc_start: 0.9004 (tpt) cc_final: 0.8582 (tpp) REVERT: G 213 MET cc_start: 0.8271 (ttp) cc_final: 0.8022 (tmm) REVERT: G 218 LEU cc_start: 0.9275 (mt) cc_final: 0.9012 (mt) REVERT: G 278 HIS cc_start: 0.8843 (t-90) cc_final: 0.8633 (t-90) REVERT: G 349 GLU cc_start: 0.8569 (pm20) cc_final: 0.7955 (pm20) REVERT: G 351 LEU cc_start: 0.9562 (tp) cc_final: 0.9246 (tp) REVERT: G 387 LEU cc_start: 0.8713 (mt) cc_final: 0.8465 (mt) REVERT: G 473 MET cc_start: 0.8030 (ptm) cc_final: 0.7818 (ttp) REVERT: G 528 LEU cc_start: 0.9205 (mt) cc_final: 0.8943 (mt) REVERT: G 626 LEU cc_start: 0.8693 (tp) cc_final: 0.8490 (tp) REVERT: G 643 ARG cc_start: 0.8956 (mmt90) cc_final: 0.8016 (tmm-80) REVERT: H 17 MET cc_start: 0.9586 (tmm) cc_final: 0.8751 (tmm) REVERT: H 35 LYS cc_start: 0.8746 (mmtp) cc_final: 0.8468 (mmtp) REVERT: H 53 MET cc_start: 0.9140 (ttt) cc_final: 0.8694 (ttt) REVERT: H 57 MET cc_start: 0.7800 (mtp) cc_final: 0.7094 (mtp) REVERT: H 71 PHE cc_start: 0.7204 (t80) cc_final: 0.6827 (t80) REVERT: H 83 LEU cc_start: 0.9492 (mt) cc_final: 0.9205 (mt) REVERT: H 84 SER cc_start: 0.9630 (m) cc_final: 0.9363 (p) REVERT: H 85 LEU cc_start: 0.7926 (mt) cc_final: 0.7619 (mt) REVERT: H 133 LEU cc_start: 0.9682 (mt) cc_final: 0.9452 (pp) REVERT: H 134 ARG cc_start: 0.9037 (mmm-85) cc_final: 0.8737 (mmm-85) REVERT: H 183 MET cc_start: 0.9218 (mtt) cc_final: 0.8624 (mtt) REVERT: H 192 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8595 (tm-30) REVERT: H 225 MET cc_start: 0.8800 (mmm) cc_final: 0.8529 (mmt) REVERT: H 227 GLU cc_start: 0.9153 (tp30) cc_final: 0.8769 (tp30) REVERT: H 231 ILE cc_start: 0.9811 (mt) cc_final: 0.9040 (mt) REVERT: H 234 MET cc_start: 0.9515 (mmm) cc_final: 0.9097 (mmm) REVERT: H 238 THR cc_start: 0.9276 (m) cc_final: 0.9002 (p) REVERT: H 240 ILE cc_start: 0.9493 (mm) cc_final: 0.9265 (mm) REVERT: I 48 VAL cc_start: 0.4635 (m) cc_final: 0.4277 (t) REVERT: I 73 THR cc_start: 0.9671 (p) cc_final: 0.9275 (p) REVERT: I 159 GLN cc_start: 0.9181 (tp40) cc_final: 0.8926 (tp40) REVERT: I 195 ASP cc_start: 0.8948 (m-30) cc_final: 0.8712 (m-30) REVERT: P 76 MET cc_start: 0.8739 (ppp) cc_final: 0.8276 (ppp) REVERT: P 233 PHE cc_start: 0.7295 (m-80) cc_final: 0.6982 (m-80) REVERT: P 328 MET cc_start: 0.7387 (pmm) cc_final: 0.6918 (pmm) REVERT: P 348 LYS cc_start: 0.8034 (mmtm) cc_final: 0.6793 (mttt) REVERT: Q 69 GLU cc_start: 0.8798 (tp30) cc_final: 0.8559 (tp30) REVERT: Q 112 MET cc_start: 0.8291 (mmm) cc_final: 0.7418 (mmm) REVERT: Q 126 LEU cc_start: 0.8994 (tp) cc_final: 0.8546 (tt) REVERT: Q 141 ASN cc_start: 0.9258 (m110) cc_final: 0.8610 (m110) REVERT: T 113 LEU cc_start: 0.9168 (mm) cc_final: 0.8780 (mm) REVERT: V 79 GLU cc_start: 0.8975 (mp0) cc_final: 0.8772 (mp0) REVERT: V 93 LYS cc_start: 0.9240 (mtmm) cc_final: 0.8970 (mttt) REVERT: W 78 ASP cc_start: 0.8885 (t70) cc_final: 0.8630 (t70) REVERT: W 85 LEU cc_start: 0.9452 (mt) cc_final: 0.9207 (mt) REVERT: W 94 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8848 (mm-40) REVERT: W 95 GLU cc_start: 0.8390 (tp30) cc_final: 0.8051 (tp30) REVERT: W 107 MET cc_start: 0.8988 (mmt) cc_final: 0.8518 (mmm) REVERT: W 127 MET cc_start: 0.7343 (tpp) cc_final: 0.7030 (mmm) REVERT: X 71 PHE cc_start: 0.8084 (m-10) cc_final: 0.7601 (m-80) REVERT: Z 10 MET cc_start: 0.8407 (mmm) cc_final: 0.7833 (mmt) REVERT: Z 72 MET cc_start: 0.8661 (mmt) cc_final: 0.8413 (mmt) REVERT: a 9 LEU cc_start: 0.8919 (pp) cc_final: 0.8642 (mt) REVERT: a 26 ILE cc_start: 0.9340 (mt) cc_final: 0.9062 (tp) REVERT: q 91 HIS cc_start: 0.8332 (m-70) cc_final: 0.8079 (m90) REVERT: q 127 TYR cc_start: 0.9068 (p90) cc_final: 0.8165 (p90) REVERT: r 93 LYS cc_start: 0.8425 (mppt) cc_final: 0.7775 (mmmt) outliers start: 2 outliers final: 2 residues processed: 876 average time/residue: 0.1876 time to fit residues: 267.3592 Evaluate side-chains 665 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 663 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 336 optimal weight: 2.9990 chunk 361 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 246 optimal weight: 5.9990 chunk 341 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 330 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 156 optimal weight: 0.0270 chunk 136 optimal weight: 9.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- 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 166 ASN ** 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 ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 132 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN S 22 HIS ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 54 ASN ** b 69 HIS ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.080802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.065212 restraints weight = 178790.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.067058 restraints weight = 116790.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.068348 restraints weight = 86037.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.069229 restraints weight = 68942.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.069926 restraints weight = 59124.490| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.6796 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= 0.162 Angle : 0.958 77.407 46909 Z= 0.360 Chirality : 0.045 0.185 5135 Planarity : 0.005 0.061 5952 Dihedral : 7.732 147.512 4761 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.12 % Favored : 95.86 % Rotamer: Outliers : 0.11 % Allowed : 2.37 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.13), residues: 4127 helix: 0.45 (0.12), residues: 1878 sheet: -0.93 (0.27), residues: 367 loop : -0.84 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 51 TYR 0.021 0.002 TYR D 141 PHE 0.040 0.002 PHE H 224 TRP 0.044 0.002 TRP V 97 HIS 0.008 0.001 HIS F 422 Details of bonding type rmsd covalent geometry : bond 0.00353 (34542) covalent geometry : angle 0.70085 (46822) SS BOND : bond 0.00463 ( 3) SS BOND : angle 1.37841 ( 6) hydrogen bonds : bond 0.04249 ( 1439) hydrogen bonds : angle 5.18505 ( 4155) metal coordination : bond 0.01970 ( 33) metal coordination : angle 15.72107 ( 81) *********************** 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 872 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 868 time to evaluate : 1.314 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 88 MET cc_start: 0.9057 (tpp) cc_final: 0.8504 (ttt) REVERT: A 89 ILE cc_start: 0.7723 (pt) cc_final: 0.7455 (pt) REVERT: B 86 ARG cc_start: 0.8746 (mtt90) cc_final: 0.8255 (mtt90) REVERT: B 131 MET cc_start: 0.8804 (tpp) cc_final: 0.8594 (tpt) REVERT: B 132 ILE cc_start: 0.8488 (pt) cc_final: 0.8093 (pt) REVERT: B 206 LEU cc_start: 0.9413 (tt) cc_final: 0.9184 (tt) REVERT: C 118 VAL cc_start: 0.9539 (t) cc_final: 0.9226 (m) REVERT: C 172 MET cc_start: 0.8440 (tpp) cc_final: 0.7879 (tpp) REVERT: C 227 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7439 (tp40) REVERT: C 229 PHE cc_start: 0.9096 (t80) cc_final: 0.8859 (t80) REVERT: D 185 MET cc_start: 0.9280 (tpp) cc_final: 0.8977 (tpp) REVERT: D 190 HIS cc_start: 0.8550 (t-170) cc_final: 0.8300 (t70) REVERT: D 197 MET cc_start: 0.9244 (pmm) cc_final: 0.8906 (pmm) REVERT: D 203 MET cc_start: 0.9380 (mmp) cc_final: 0.9136 (mmp) REVERT: D 210 MET cc_start: 0.9243 (mtm) cc_final: 0.8764 (mtm) REVERT: D 251 PHE cc_start: 0.9063 (t80) cc_final: 0.8800 (t80) REVERT: D 286 TYR cc_start: 0.8637 (m-80) cc_final: 0.8383 (m-80) REVERT: D 377 SER cc_start: 0.9443 (m) cc_final: 0.9217 (t) REVERT: D 443 MET cc_start: 0.9058 (mmp) cc_final: 0.8542 (mmp) REVERT: D 456 ILE cc_start: 0.9214 (mm) cc_final: 0.8743 (pt) REVERT: E 110 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7755 (mmm-85) REVERT: E 113 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: E 118 TYR cc_start: 0.8188 (m-80) cc_final: 0.7958 (m-80) REVERT: E 242 PHE cc_start: 0.7143 (p90) cc_final: 0.6438 (p90) REVERT: F 62 TRP cc_start: 0.7895 (t60) cc_final: 0.7635 (t60) REVERT: F 63 TYR cc_start: 0.5764 (t80) cc_final: 0.5217 (t80) REVERT: F 136 HIS cc_start: 0.8320 (m-70) cc_final: 0.8062 (m-70) REVERT: F 149 MET cc_start: 0.7073 (mmm) cc_final: 0.6440 (mmt) REVERT: F 292 MET cc_start: 0.7200 (mtm) cc_final: 0.6952 (mtt) REVERT: G 39 GLN cc_start: 0.8912 (tp40) cc_final: 0.8230 (tm-30) REVERT: G 42 MET cc_start: 0.8313 (tpp) cc_final: 0.8004 (tpp) REVERT: G 77 MET cc_start: 0.9102 (tpt) cc_final: 0.8702 (tpp) REVERT: G 213 MET cc_start: 0.8163 (ttp) cc_final: 0.7901 (tmm) REVERT: G 218 LEU cc_start: 0.9287 (mt) cc_final: 0.9021 (mt) REVERT: G 278 HIS cc_start: 0.8795 (t-90) cc_final: 0.8572 (t-170) REVERT: G 354 LEU cc_start: 0.9785 (tp) cc_final: 0.9529 (tt) REVERT: G 387 LEU cc_start: 0.8768 (mt) cc_final: 0.8343 (mt) REVERT: G 473 MET cc_start: 0.8176 (ptm) cc_final: 0.7906 (ttp) REVERT: G 643 ARG cc_start: 0.8981 (mmt90) cc_final: 0.8050 (tmm-80) REVERT: H 17 MET cc_start: 0.9502 (tmm) cc_final: 0.8627 (tmm) REVERT: H 53 MET cc_start: 0.9202 (ttt) cc_final: 0.8823 (ttt) REVERT: H 71 PHE cc_start: 0.7209 (t80) cc_final: 0.6804 (t80) REVERT: H 79 LEU cc_start: 0.9551 (tp) cc_final: 0.9341 (tp) REVERT: H 83 LEU cc_start: 0.9519 (mt) cc_final: 0.9209 (mt) REVERT: H 84 SER cc_start: 0.9641 (m) cc_final: 0.9418 (p) REVERT: H 133 LEU cc_start: 0.9706 (mt) cc_final: 0.9474 (pp) REVERT: H 183 MET cc_start: 0.9297 (mtt) cc_final: 0.8674 (mtt) REVERT: H 192 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8618 (tm-30) REVERT: H 193 THR cc_start: 0.8950 (p) cc_final: 0.8424 (p) REVERT: H 195 ARG cc_start: 0.8874 (mmp80) cc_final: 0.8325 (mmm160) REVERT: H 225 MET cc_start: 0.8440 (mmm) cc_final: 0.8203 (mmt) REVERT: H 227 GLU cc_start: 0.9189 (tp30) cc_final: 0.8817 (tp30) REVERT: H 238 THR cc_start: 0.9346 (m) cc_final: 0.9039 (p) REVERT: H 240 ILE cc_start: 0.9513 (mm) cc_final: 0.9306 (mm) REVERT: I 48 VAL cc_start: 0.4493 (m) cc_final: 0.4157 (t) REVERT: I 73 THR cc_start: 0.9568 (p) cc_final: 0.9307 (p) REVERT: I 90 LYS cc_start: 0.8336 (mmmt) cc_final: 0.8057 (tppt) REVERT: I 151 LYS cc_start: 0.9471 (mttm) cc_final: 0.9229 (mmtp) REVERT: I 177 THR cc_start: 0.8871 (p) cc_final: 0.8269 (p) REVERT: I 179 THR cc_start: 0.9005 (p) cc_final: 0.8693 (p) REVERT: I 195 ASP cc_start: 0.8946 (m-30) cc_final: 0.8693 (m-30) REVERT: P 48 ARG cc_start: 0.6186 (tpp80) cc_final: 0.4834 (tpp-160) REVERT: P 76 MET cc_start: 0.8682 (ppp) cc_final: 0.8163 (ppp) REVERT: P 233 PHE cc_start: 0.7330 (m-80) cc_final: 0.7034 (m-80) REVERT: P 335 LEU cc_start: 0.8515 (mm) cc_final: 0.8164 (tp) REVERT: P 345 LEU cc_start: 0.8528 (tt) cc_final: 0.8043 (mp) REVERT: P 348 LYS cc_start: 0.8078 (mmtm) cc_final: 0.6734 (mttp) REVERT: Q 69 GLU cc_start: 0.8807 (tp30) cc_final: 0.8575 (tp30) REVERT: Q 85 ASN cc_start: 0.9282 (p0) cc_final: 0.8856 (p0) REVERT: Q 86 ASN cc_start: 0.8726 (m-40) cc_final: 0.8468 (m-40) REVERT: Q 111 LEU cc_start: 0.9097 (pp) cc_final: 0.8879 (pp) REVERT: Q 112 MET cc_start: 0.8325 (mmm) cc_final: 0.7320 (mmm) REVERT: Q 126 LEU cc_start: 0.9048 (tp) cc_final: 0.8817 (tt) REVERT: Q 137 PHE cc_start: 0.8798 (t80) cc_final: 0.8237 (t80) REVERT: Q 141 ASN cc_start: 0.9092 (m110) cc_final: 0.8664 (m110) REVERT: Q 156 LYS cc_start: 0.8371 (mmpt) cc_final: 0.7888 (mmmt) REVERT: S 20 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7459 (mtm110) REVERT: T 80 LYS cc_start: 0.8687 (tmtt) cc_final: 0.8077 (mptt) REVERT: T 113 LEU cc_start: 0.9110 (mm) cc_final: 0.8742 (mm) REVERT: T 122 MET cc_start: 0.8401 (ptp) cc_final: 0.7645 (ppp) REVERT: T 133 ILE cc_start: 0.8802 (pt) cc_final: 0.8285 (pt) REVERT: V 79 GLU cc_start: 0.9022 (mp0) cc_final: 0.8815 (mp0) REVERT: V 93 LYS cc_start: 0.9258 (mtmm) cc_final: 0.9006 (mttt) REVERT: W 71 MET cc_start: 0.8669 (mmm) cc_final: 0.8299 (mmm) REVERT: W 78 ASP cc_start: 0.8901 (t70) cc_final: 0.8635 (t70) REVERT: W 85 LEU cc_start: 0.9463 (mt) cc_final: 0.9217 (mt) REVERT: W 94 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8958 (mm-40) REVERT: W 95 GLU cc_start: 0.8575 (tp30) cc_final: 0.8138 (tp30) REVERT: W 127 MET cc_start: 0.7334 (tpp) cc_final: 0.7082 (mmm) REVERT: X 71 PHE cc_start: 0.8099 (m-10) cc_final: 0.7635 (m-80) REVERT: Z 10 MET cc_start: 0.8438 (mmm) cc_final: 0.7858 (mmt) REVERT: a 12 MET cc_start: 0.9093 (ttm) cc_final: 0.8866 (tpp) REVERT: a 26 ILE cc_start: 0.9356 (mt) cc_final: 0.9107 (tp) REVERT: q 91 HIS cc_start: 0.8392 (m-70) cc_final: 0.8015 (m90) REVERT: q 127 TYR cc_start: 0.9045 (p90) cc_final: 0.8130 (p90) REVERT: r 93 LYS cc_start: 0.8342 (mppt) cc_final: 0.7693 (mmmt) outliers start: 4 outliers final: 1 residues processed: 871 average time/residue: 0.2004 time to fit residues: 284.5731 Evaluate side-chains 661 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 659 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 198 optimal weight: 30.0000 chunk 120 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 103 optimal weight: 0.0030 chunk 170 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 222 optimal weight: 0.0470 overall best weight: 1.1690 ------------------------------------------------------------------------------- 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 166 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN P 71 ASN Q 51 GLN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 46 ASN q 59 HIS ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.081253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.065268 restraints weight = 180489.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.067198 restraints weight = 115342.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.068620 restraints weight = 84340.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.069635 restraints weight = 66846.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.070339 restraints weight = 56289.821| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34578 Z= 0.144 Angle : 0.948 77.400 46909 Z= 0.361 Chirality : 0.045 0.277 5135 Planarity : 0.005 0.060 5952 Dihedral : 7.610 150.207 4761 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.08 % Allowed : 1.46 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.13), residues: 4127 helix: 0.42 (0.12), residues: 1883 sheet: -0.95 (0.27), residues: 361 loop : -0.80 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 51 TYR 0.027 0.002 TYR B 170 PHE 0.032 0.002 PHE H 224 TRP 0.056 0.002 TRP a 45 HIS 0.011 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00328 (34542) covalent geometry : angle 0.70264 (46822) SS BOND : bond 0.00427 ( 3) SS BOND : angle 2.29772 ( 6) hydrogen bonds : bond 0.04202 ( 1439) hydrogen bonds : angle 5.11672 ( 4155) metal coordination : bond 0.01609 ( 33) metal coordination : angle 15.33066 ( 81) *********************** 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 865 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 862 time to evaluate : 1.015 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 88 MET cc_start: 0.9076 (tpp) cc_final: 0.8114 (tpt) REVERT: A 95 VAL cc_start: 0.8347 (t) cc_final: 0.8049 (t) REVERT: B 103 GLU cc_start: 0.8933 (tp30) cc_final: 0.8691 (tp30) REVERT: B 129 ASP cc_start: 0.7342 (t0) cc_final: 0.6383 (m-30) REVERT: B 131 MET cc_start: 0.8775 (tpp) cc_final: 0.8571 (tpp) REVERT: C 118 VAL cc_start: 0.9533 (t) cc_final: 0.9233 (m) REVERT: C 166 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8354 (mt-10) REVERT: C 168 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8677 (tm-30) REVERT: C 172 MET cc_start: 0.8224 (tpp) cc_final: 0.7768 (tpp) REVERT: C 229 PHE cc_start: 0.9005 (t80) cc_final: 0.8769 (t80) REVERT: C 241 PHE cc_start: 0.7126 (p90) cc_final: 0.6868 (p90) REVERT: D 145 MET cc_start: 0.9198 (mpp) cc_final: 0.8301 (mpp) REVERT: D 185 MET cc_start: 0.9164 (tpp) cc_final: 0.8822 (tpp) REVERT: D 197 MET cc_start: 0.9180 (pmm) cc_final: 0.8822 (pmm) REVERT: D 200 PHE cc_start: 0.8160 (t80) cc_final: 0.7822 (t80) REVERT: D 210 MET cc_start: 0.9176 (mtm) cc_final: 0.8744 (mtm) REVERT: D 251 PHE cc_start: 0.9002 (t80) cc_final: 0.8739 (t80) REVERT: D 286 TYR cc_start: 0.8546 (m-80) cc_final: 0.8098 (m-80) REVERT: D 377 SER cc_start: 0.9442 (m) cc_final: 0.9226 (t) REVERT: D 443 MET cc_start: 0.9053 (mmp) cc_final: 0.8569 (mmp) REVERT: D 456 ILE cc_start: 0.9158 (mm) cc_final: 0.8622 (pt) REVERT: E 109 MET cc_start: 0.6907 (tpt) cc_final: 0.6277 (tmm) REVERT: E 242 PHE cc_start: 0.7110 (p90) cc_final: 0.6357 (p90) REVERT: F 62 TRP cc_start: 0.7915 (t60) cc_final: 0.7635 (t60) REVERT: F 136 HIS cc_start: 0.8198 (m-70) cc_final: 0.7942 (m-70) REVERT: F 149 MET cc_start: 0.7134 (mmm) cc_final: 0.5924 (mmm) REVERT: F 292 MET cc_start: 0.7315 (mtm) cc_final: 0.7108 (mtt) REVERT: G 39 GLN cc_start: 0.8905 (tp40) cc_final: 0.8243 (tm-30) REVERT: G 77 MET cc_start: 0.8986 (tpt) cc_final: 0.8628 (tpp) REVERT: G 218 LEU cc_start: 0.9221 (mt) cc_final: 0.8949 (mt) REVERT: G 333 PHE cc_start: 0.8281 (m-10) cc_final: 0.7985 (m-10) REVERT: G 349 GLU cc_start: 0.8445 (pm20) cc_final: 0.7914 (pm20) REVERT: G 387 LEU cc_start: 0.8715 (mt) cc_final: 0.8269 (mt) REVERT: G 473 MET cc_start: 0.8156 (ptm) cc_final: 0.7901 (ttp) REVERT: G 544 MET cc_start: 0.8356 (mmm) cc_final: 0.8067 (mmp) REVERT: G 579 MET cc_start: 0.9113 (tpp) cc_final: 0.8763 (tpt) REVERT: G 639 LEU cc_start: 0.9210 (tt) cc_final: 0.8985 (tt) REVERT: G 643 ARG cc_start: 0.8969 (mmt90) cc_final: 0.8047 (tmm-80) REVERT: G 684 LEU cc_start: 0.8022 (pp) cc_final: 0.7748 (mp) REVERT: G 707 MET cc_start: 0.8986 (mmm) cc_final: 0.8400 (mmm) REVERT: H 17 MET cc_start: 0.9501 (tmm) cc_final: 0.8770 (tmm) REVERT: H 53 MET cc_start: 0.9195 (ttt) cc_final: 0.8738 (ttt) REVERT: H 71 PHE cc_start: 0.7126 (t80) cc_final: 0.6761 (t80) REVERT: H 79 LEU cc_start: 0.9582 (tp) cc_final: 0.9347 (tp) REVERT: H 83 LEU cc_start: 0.9525 (mt) cc_final: 0.9229 (mt) REVERT: H 85 LEU cc_start: 0.8007 (mt) cc_final: 0.7797 (mt) REVERT: H 133 LEU cc_start: 0.9692 (mt) cc_final: 0.9467 (pp) REVERT: H 183 MET cc_start: 0.9290 (mtt) cc_final: 0.8707 (mtt) REVERT: H 192 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8525 (tm-30) REVERT: H 193 THR cc_start: 0.8975 (p) cc_final: 0.8434 (p) REVERT: H 195 ARG cc_start: 0.8883 (mmp80) cc_final: 0.8452 (mmm160) REVERT: H 227 GLU cc_start: 0.9172 (tp30) cc_final: 0.8831 (tp30) REVERT: H 231 ILE cc_start: 0.9688 (mt) cc_final: 0.9480 (mt) REVERT: H 238 THR cc_start: 0.9335 (m) cc_final: 0.9021 (p) REVERT: H 240 ILE cc_start: 0.9512 (mm) cc_final: 0.9295 (mm) REVERT: I 48 VAL cc_start: 0.4391 (m) cc_final: 0.4096 (t) REVERT: I 195 ASP cc_start: 0.8916 (m-30) cc_final: 0.8688 (m-30) REVERT: P 76 MET cc_start: 0.8702 (ppp) cc_final: 0.8282 (ppp) REVERT: P 214 LEU cc_start: 0.8684 (tt) cc_final: 0.8433 (tt) REVERT: P 233 PHE cc_start: 0.7506 (m-80) cc_final: 0.7192 (m-80) REVERT: P 335 LEU cc_start: 0.8677 (mm) cc_final: 0.8453 (mp) REVERT: P 345 LEU cc_start: 0.8487 (tt) cc_final: 0.8014 (mp) REVERT: P 347 LEU cc_start: 0.8795 (mp) cc_final: 0.8591 (mp) REVERT: P 348 LYS cc_start: 0.8078 (mmtm) cc_final: 0.6760 (mttp) REVERT: Q 85 ASN cc_start: 0.9218 (p0) cc_final: 0.8815 (p0) REVERT: Q 86 ASN cc_start: 0.8654 (m-40) cc_final: 0.8442 (m-40) REVERT: Q 112 MET cc_start: 0.8217 (mmm) cc_final: 0.7153 (mmm) REVERT: Q 126 LEU cc_start: 0.8916 (tp) cc_final: 0.8598 (tt) REVERT: Q 137 PHE cc_start: 0.8805 (t80) cc_final: 0.8123 (t80) REVERT: Q 140 LYS cc_start: 0.9165 (ptpp) cc_final: 0.8776 (ptmm) REVERT: Q 141 ASN cc_start: 0.9061 (m110) cc_final: 0.8384 (m110) REVERT: Q 149 GLU cc_start: 0.8786 (pm20) cc_final: 0.8581 (pm20) REVERT: Q 156 LYS cc_start: 0.8257 (mmpt) cc_final: 0.7958 (mmmt) REVERT: T 80 LYS cc_start: 0.8669 (tmmt) cc_final: 0.8285 (mptt) REVERT: T 113 LEU cc_start: 0.9135 (mm) cc_final: 0.8779 (mm) REVERT: T 122 MET cc_start: 0.8540 (ptp) cc_final: 0.7650 (ppp) REVERT: T 133 ILE cc_start: 0.8740 (pt) cc_final: 0.8345 (pt) REVERT: V 79 GLU cc_start: 0.9041 (mp0) cc_final: 0.8817 (mp0) REVERT: V 93 LYS cc_start: 0.9220 (mtmm) cc_final: 0.8973 (mttt) REVERT: W 71 MET cc_start: 0.8681 (mmm) cc_final: 0.8330 (mmm) REVERT: W 78 ASP cc_start: 0.8889 (t70) cc_final: 0.8610 (t70) REVERT: W 85 LEU cc_start: 0.9449 (mt) cc_final: 0.9208 (mt) REVERT: W 95 GLU cc_start: 0.8520 (tp30) cc_final: 0.8229 (tp30) REVERT: W 107 MET cc_start: 0.8859 (mmt) cc_final: 0.8361 (mmm) REVERT: W 127 MET cc_start: 0.7406 (tpp) cc_final: 0.7183 (mmm) REVERT: X 71 PHE cc_start: 0.8029 (m-10) cc_final: 0.7631 (m-80) REVERT: X 97 PHE cc_start: 0.8086 (m-10) cc_final: 0.7878 (m-10) REVERT: Z 10 MET cc_start: 0.8539 (mmm) cc_final: 0.7924 (mmt) REVERT: Z 50 MET cc_start: 0.9430 (ptp) cc_final: 0.9196 (ptp) REVERT: Z 72 MET cc_start: 0.9183 (mmt) cc_final: 0.8762 (mmt) REVERT: Z 75 PHE cc_start: 0.9139 (m-80) cc_final: 0.8643 (m-80) REVERT: a 5 ILE cc_start: 0.9294 (mp) cc_final: 0.8828 (mm) REVERT: a 12 MET cc_start: 0.9043 (ttm) cc_final: 0.8819 (tpp) REVERT: a 26 ILE cc_start: 0.9380 (mt) cc_final: 0.9116 (tp) REVERT: q 91 HIS cc_start: 0.8320 (m-70) cc_final: 0.8087 (m90) REVERT: q 127 TYR cc_start: 0.8929 (p90) cc_final: 0.8160 (p90) REVERT: r 93 LYS cc_start: 0.8374 (mppt) cc_final: 0.7773 (mmmt) outliers start: 3 outliers final: 1 residues processed: 865 average time/residue: 0.1829 time to fit residues: 256.3955 Evaluate side-chains 672 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 671 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 290 optimal weight: 0.0040 chunk 335 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 379 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 276 optimal weight: 8.9990 chunk 272 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- 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 166 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 190 HIS E 58 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN Q 51 GLN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.081012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.065412 restraints weight = 178929.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067267 restraints weight = 116861.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.068579 restraints weight = 85755.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.069540 restraints weight = 68525.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.070167 restraints weight = 58089.448| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.7311 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= 0.146 Angle : 0.951 78.717 46909 Z= 0.364 Chirality : 0.045 0.231 5135 Planarity : 0.005 0.061 5952 Dihedral : 7.517 152.747 4761 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.13), residues: 4127 helix: 0.42 (0.12), residues: 1887 sheet: -0.93 (0.28), residues: 339 loop : -0.79 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 51 TYR 0.024 0.002 TYR E 118 PHE 0.053 0.002 PHE C 197 TRP 0.111 0.002 TRP H 118 HIS 0.006 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00333 (34542) covalent geometry : angle 0.70734 (46822) SS BOND : bond 0.00407 ( 3) SS BOND : angle 1.87142 ( 6) hydrogen bonds : bond 0.04106 ( 1439) hydrogen bonds : angle 5.15985 ( 4155) metal coordination : bond 0.01575 ( 33) metal coordination : angle 15.29074 ( 81) *********************** 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 852 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 850 time to evaluate : 0.890 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 87 MET cc_start: 0.7984 (mmp) cc_final: 0.7740 (mmm) REVERT: A 88 MET cc_start: 0.8976 (tpp) cc_final: 0.7994 (tpt) REVERT: A 92 PHE cc_start: 0.7831 (m-10) cc_final: 0.7479 (m-10) REVERT: A 95 VAL cc_start: 0.8314 (t) cc_final: 0.8058 (t) REVERT: B 103 GLU cc_start: 0.8989 (tp30) cc_final: 0.8776 (tp30) REVERT: B 129 ASP cc_start: 0.7829 (t0) cc_final: 0.6744 (m-30) REVERT: B 131 MET cc_start: 0.8787 (tpp) cc_final: 0.8458 (tpt) REVERT: C 118 VAL cc_start: 0.9551 (t) cc_final: 0.9264 (m) REVERT: C 166 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8333 (mt-10) REVERT: C 227 GLN cc_start: 0.7837 (tp40) cc_final: 0.7537 (tp40) REVERT: C 229 PHE cc_start: 0.9157 (t80) cc_final: 0.8342 (t80) REVERT: C 241 PHE cc_start: 0.7296 (p90) cc_final: 0.6928 (p90) REVERT: D 145 MET cc_start: 0.9104 (mpp) cc_final: 0.8755 (mpp) REVERT: D 148 GLU cc_start: 0.8070 (pt0) cc_final: 0.7628 (pt0) REVERT: D 185 MET cc_start: 0.9222 (tpp) cc_final: 0.9004 (tpp) REVERT: D 197 MET cc_start: 0.9196 (pmm) cc_final: 0.8642 (pmm) REVERT: D 210 MET cc_start: 0.9218 (mtm) cc_final: 0.8805 (mtm) REVERT: D 251 PHE cc_start: 0.9041 (t80) cc_final: 0.8764 (t80) REVERT: D 286 TYR cc_start: 0.8439 (m-80) cc_final: 0.8227 (m-80) REVERT: D 336 GLU cc_start: 0.9278 (mm-30) cc_final: 0.9033 (mm-30) REVERT: D 377 SER cc_start: 0.9420 (m) cc_final: 0.9209 (t) REVERT: D 443 MET cc_start: 0.9100 (mmp) cc_final: 0.8609 (mmp) REVERT: D 456 ILE cc_start: 0.9101 (mm) cc_final: 0.8777 (pt) REVERT: E 89 ASN cc_start: 0.8772 (t0) cc_final: 0.8552 (t0) REVERT: E 109 MET cc_start: 0.7014 (tpt) cc_final: 0.6691 (tmm) REVERT: E 167 LEU cc_start: 0.8867 (mm) cc_final: 0.8638 (mm) REVERT: E 184 MET cc_start: 0.8772 (ptt) cc_final: 0.8367 (ptt) REVERT: E 242 PHE cc_start: 0.7064 (p90) cc_final: 0.6341 (p90) REVERT: F 62 TRP cc_start: 0.7865 (t60) cc_final: 0.7610 (t60) REVERT: F 136 HIS cc_start: 0.8130 (m-70) cc_final: 0.7911 (m-70) REVERT: F 149 MET cc_start: 0.7238 (mmm) cc_final: 0.5983 (mmm) REVERT: F 208 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8643 (tm-30) REVERT: F 262 PHE cc_start: 0.8591 (t80) cc_final: 0.8260 (t80) REVERT: F 422 HIS cc_start: 0.8374 (m90) cc_final: 0.8011 (m90) REVERT: G 39 GLN cc_start: 0.8952 (tp40) cc_final: 0.8255 (tm-30) REVERT: G 77 MET cc_start: 0.9066 (tpt) cc_final: 0.8598 (tpp) REVERT: G 117 MET cc_start: 0.8715 (tpp) cc_final: 0.8382 (tpp) REVERT: G 218 LEU cc_start: 0.9254 (mt) cc_final: 0.8968 (mt) REVERT: G 333 PHE cc_start: 0.8252 (m-10) cc_final: 0.7909 (m-10) REVERT: G 349 GLU cc_start: 0.8439 (pm20) cc_final: 0.7913 (pm20) REVERT: G 354 LEU cc_start: 0.9795 (tp) cc_final: 0.9551 (tt) REVERT: G 387 LEU cc_start: 0.8700 (mt) cc_final: 0.8261 (mt) REVERT: G 544 MET cc_start: 0.8485 (mmm) cc_final: 0.8166 (mmp) REVERT: G 643 ARG cc_start: 0.8964 (mmt90) cc_final: 0.8050 (tmm-80) REVERT: G 707 MET cc_start: 0.8956 (mmm) cc_final: 0.8675 (mmm) REVERT: H 53 MET cc_start: 0.9214 (ttt) cc_final: 0.8859 (ttt) REVERT: H 71 PHE cc_start: 0.7223 (t80) cc_final: 0.6902 (t80) REVERT: H 83 LEU cc_start: 0.9523 (mt) cc_final: 0.9213 (mt) REVERT: H 133 LEU cc_start: 0.9688 (mt) cc_final: 0.9480 (pp) REVERT: H 183 MET cc_start: 0.9316 (mtt) cc_final: 0.8721 (mtt) REVERT: H 185 TRP cc_start: 0.8774 (t-100) cc_final: 0.8365 (t-100) REVERT: H 192 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8484 (tm-30) REVERT: H 195 ARG cc_start: 0.9164 (mmp80) cc_final: 0.8478 (mmm160) REVERT: H 225 MET cc_start: 0.8779 (tpp) cc_final: 0.8541 (tpp) REVERT: H 227 GLU cc_start: 0.9185 (tp30) cc_final: 0.8853 (tp30) REVERT: H 238 THR cc_start: 0.9329 (m) cc_final: 0.8904 (p) REVERT: H 280 PHE cc_start: 0.8876 (m-80) cc_final: 0.8610 (m-80) REVERT: H 288 LEU cc_start: 0.9510 (mm) cc_final: 0.9309 (mm) REVERT: I 48 VAL cc_start: 0.4448 (m) cc_final: 0.4069 (t) REVERT: I 151 LYS cc_start: 0.9422 (mttm) cc_final: 0.9186 (mmtt) REVERT: I 195 ASP cc_start: 0.8944 (m-30) cc_final: 0.8701 (m-30) REVERT: P 76 MET cc_start: 0.8683 (ppp) cc_final: 0.8093 (ppp) REVERT: P 233 PHE cc_start: 0.7453 (m-80) cc_final: 0.7144 (m-80) REVERT: P 345 LEU cc_start: 0.8475 (tt) cc_final: 0.8012 (mp) REVERT: P 348 LYS cc_start: 0.8074 (mmtm) cc_final: 0.6740 (mmtp) REVERT: Q 69 GLU cc_start: 0.8821 (tp30) cc_final: 0.8368 (tp30) REVERT: Q 85 ASN cc_start: 0.9289 (p0) cc_final: 0.8815 (p0) REVERT: Q 86 ASN cc_start: 0.8650 (m-40) cc_final: 0.8285 (m-40) REVERT: Q 101 PHE cc_start: 0.8338 (m-10) cc_final: 0.7868 (m-80) REVERT: Q 105 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7254 (tm-30) REVERT: Q 112 MET cc_start: 0.8337 (mmm) cc_final: 0.7166 (mmm) REVERT: Q 114 TRP cc_start: 0.8039 (m-10) cc_final: 0.7716 (m-10) REVERT: Q 126 LEU cc_start: 0.8978 (tp) cc_final: 0.8657 (tt) REVERT: Q 137 PHE cc_start: 0.8841 (t80) cc_final: 0.8208 (t80) REVERT: Q 140 LYS cc_start: 0.9138 (ptpp) cc_final: 0.8748 (ptmm) REVERT: Q 141 ASN cc_start: 0.8975 (m110) cc_final: 0.8258 (m110) REVERT: Q 156 LYS cc_start: 0.8437 (mmpt) cc_final: 0.7941 (mmmt) REVERT: T 80 LYS cc_start: 0.8633 (tmmt) cc_final: 0.8161 (mptt) REVERT: T 113 LEU cc_start: 0.9174 (mm) cc_final: 0.8813 (mm) REVERT: T 122 MET cc_start: 0.8491 (ptp) cc_final: 0.7597 (ppp) REVERT: T 133 ILE cc_start: 0.8766 (pt) cc_final: 0.8370 (pt) REVERT: W 68 GLU cc_start: 0.9057 (mp0) cc_final: 0.8826 (mp0) REVERT: W 78 ASP cc_start: 0.8894 (t70) cc_final: 0.8625 (t70) REVERT: W 85 LEU cc_start: 0.9460 (mt) cc_final: 0.9208 (mt) REVERT: W 95 GLU cc_start: 0.8563 (tp30) cc_final: 0.8260 (tp30) REVERT: W 107 MET cc_start: 0.8897 (mmt) cc_final: 0.8345 (mmm) REVERT: W 127 MET cc_start: 0.7380 (tpp) cc_final: 0.7155 (mmm) REVERT: X 82 PHE cc_start: 0.8980 (t80) cc_final: 0.8555 (t80) REVERT: X 97 PHE cc_start: 0.8071 (m-10) cc_final: 0.7777 (m-10) REVERT: Z 10 MET cc_start: 0.8556 (mmm) cc_final: 0.7942 (mmt) REVERT: Z 50 MET cc_start: 0.9424 (ptp) cc_final: 0.9171 (ptp) REVERT: Z 72 MET cc_start: 0.9215 (mmt) cc_final: 0.8947 (mmt) REVERT: Z 75 PHE cc_start: 0.9104 (m-80) cc_final: 0.8619 (m-80) REVERT: a 12 MET cc_start: 0.9107 (ttm) cc_final: 0.8737 (tpp) REVERT: a 26 ILE cc_start: 0.9417 (mt) cc_final: 0.9164 (tp) REVERT: b 44 MET cc_start: 0.8993 (ptp) cc_final: 0.8767 (ptp) REVERT: q 91 HIS cc_start: 0.8431 (m-70) cc_final: 0.8200 (m90) REVERT: q 127 TYR cc_start: 0.8998 (p90) cc_final: 0.8184 (p90) REVERT: q 142 THR cc_start: 0.8098 (t) cc_final: 0.7888 (m) REVERT: r 93 LYS cc_start: 0.8368 (mppt) cc_final: 0.7781 (mmmt) outliers start: 2 outliers final: 1 residues processed: 852 average time/residue: 0.1763 time to fit residues: 246.1062 Evaluate side-chains 667 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 666 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 113 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 388 optimal weight: 2.9990 chunk 356 optimal weight: 0.7980 chunk 240 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 145 optimal weight: 0.4980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 166 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 HIS ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 131 GLN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 HIS E 58 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN ** F 270 ASN ** 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 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 GLN P 71 ASN Q 51 GLN W 29 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS ** q 87 HIS ** 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 = 0.3722 r_free = 0.3722 target = 0.080448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.064615 restraints weight = 181813.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.066462 restraints weight = 116811.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.067839 restraints weight = 85606.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.068806 restraints weight = 68104.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.069409 restraints weight = 57746.805| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.7507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34578 Z= 0.150 Angle : 0.953 79.398 46909 Z= 0.366 Chirality : 0.045 0.211 5135 Planarity : 0.005 0.062 5952 Dihedral : 7.478 153.218 4761 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.03 % Allowed : 0.80 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.13), residues: 4127 helix: 0.47 (0.12), residues: 1898 sheet: -0.90 (0.27), residues: 345 loop : -0.78 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 51 TYR 0.029 0.002 TYR B 170 PHE 0.063 0.002 PHE C 197 TRP 0.068 0.002 TRP C 170 HIS 0.006 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00343 (34542) covalent geometry : angle 0.70908 (46822) SS BOND : bond 0.00382 ( 3) SS BOND : angle 1.61586 ( 6) hydrogen bonds : bond 0.04101 ( 1439) hydrogen bonds : angle 5.13809 ( 4155) metal coordination : bond 0.01658 ( 33) metal coordination : angle 15.32673 ( 81) *********************** 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 842 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 841 time to evaluate : 1.108 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 87 MET cc_start: 0.7953 (mmp) cc_final: 0.7581 (mmt) REVERT: A 88 MET cc_start: 0.8961 (tpp) cc_final: 0.7932 (tpt) REVERT: A 90 MET cc_start: 0.6417 (ptt) cc_final: 0.6133 (ptt) REVERT: A 94 LEU cc_start: 0.8567 (pp) cc_final: 0.8367 (pp) REVERT: A 95 VAL cc_start: 0.8418 (t) cc_final: 0.8193 (t) REVERT: A 98 LEU cc_start: 0.8572 (mm) cc_final: 0.8264 (tp) REVERT: B 129 ASP cc_start: 0.7576 (t0) cc_final: 0.6624 (m-30) REVERT: B 211 LYS cc_start: 0.9147 (mttm) cc_final: 0.8783 (mttt) REVERT: C 118 VAL cc_start: 0.9567 (t) cc_final: 0.9282 (m) REVERT: C 166 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8296 (mt-10) REVERT: C 176 PHE cc_start: 0.8463 (t80) cc_final: 0.8126 (t80) REVERT: C 227 GLN cc_start: 0.8112 (tp40) cc_final: 0.7691 (tp40) REVERT: D 144 MET cc_start: 0.8546 (mmp) cc_final: 0.7592 (mmp) REVERT: D 185 MET cc_start: 0.9089 (tpp) cc_final: 0.8833 (tpp) REVERT: D 197 MET cc_start: 0.9182 (pmm) cc_final: 0.8940 (pmm) REVERT: D 210 MET cc_start: 0.9183 (mtm) cc_final: 0.8726 (mtm) REVERT: D 251 PHE cc_start: 0.9024 (t80) cc_final: 0.8789 (t80) REVERT: D 286 TYR cc_start: 0.8402 (m-80) cc_final: 0.8189 (m-80) REVERT: D 336 GLU cc_start: 0.9263 (mm-30) cc_final: 0.9052 (mm-30) REVERT: D 377 SER cc_start: 0.9446 (m) cc_final: 0.9206 (t) REVERT: D 443 MET cc_start: 0.9105 (mmp) cc_final: 0.8613 (mmp) REVERT: D 456 ILE cc_start: 0.9184 (mm) cc_final: 0.8666 (pt) REVERT: E 89 ASN cc_start: 0.8739 (t0) cc_final: 0.8528 (t0) REVERT: E 167 LEU cc_start: 0.8953 (mm) cc_final: 0.8565 (mp) REVERT: E 242 PHE cc_start: 0.7095 (p90) cc_final: 0.6373 (p90) REVERT: F 42 PHE cc_start: 0.8546 (t80) cc_final: 0.7472 (t80) REVERT: F 62 TRP cc_start: 0.7837 (t60) cc_final: 0.7544 (t60) REVERT: F 136 HIS cc_start: 0.8165 (m-70) cc_final: 0.7922 (m-70) REVERT: F 149 MET cc_start: 0.7265 (mmm) cc_final: 0.6123 (mmm) REVERT: F 262 PHE cc_start: 0.8679 (t80) cc_final: 0.8257 (t80) REVERT: G 39 GLN cc_start: 0.8936 (tp40) cc_final: 0.8262 (tm-30) REVERT: G 67 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8398 (tm-30) REVERT: G 77 MET cc_start: 0.8993 (tpt) cc_final: 0.8628 (tpp) REVERT: G 218 LEU cc_start: 0.9198 (mt) cc_final: 0.8899 (mt) REVERT: G 333 PHE cc_start: 0.8235 (m-10) cc_final: 0.7863 (m-10) REVERT: G 349 GLU cc_start: 0.8455 (pm20) cc_final: 0.7939 (pm20) REVERT: G 387 LEU cc_start: 0.8638 (mt) cc_final: 0.8165 (mt) REVERT: G 544 MET cc_start: 0.8481 (mmm) cc_final: 0.8165 (mmp) REVERT: G 579 MET cc_start: 0.9150 (tpp) cc_final: 0.8861 (tpt) REVERT: G 643 ARG cc_start: 0.8987 (mmt90) cc_final: 0.8087 (tmm-80) REVERT: H 53 MET cc_start: 0.9213 (ttt) cc_final: 0.8621 (ttt) REVERT: H 71 PHE cc_start: 0.7291 (t80) cc_final: 0.6990 (t80) REVERT: H 79 LEU cc_start: 0.9562 (tp) cc_final: 0.9355 (tp) REVERT: H 83 LEU cc_start: 0.9524 (mt) cc_final: 0.9234 (mt) REVERT: H 183 MET cc_start: 0.9320 (mtt) cc_final: 0.8720 (mtt) REVERT: H 185 TRP cc_start: 0.8724 (t-100) cc_final: 0.8480 (t-100) REVERT: H 192 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8386 (tm-30) REVERT: H 225 MET cc_start: 0.8852 (tpp) cc_final: 0.8538 (tpp) REVERT: H 227 GLU cc_start: 0.9127 (tp30) cc_final: 0.8857 (tp30) REVERT: H 231 ILE cc_start: 0.9694 (mt) cc_final: 0.9438 (mt) REVERT: H 240 ILE cc_start: 0.9558 (mm) cc_final: 0.9269 (mm) REVERT: H 303 TRP cc_start: 0.8584 (t-100) cc_final: 0.8288 (t-100) REVERT: I 51 LYS cc_start: 0.8568 (pttt) cc_final: 0.8154 (mtmt) REVERT: I 178 GLU cc_start: 0.8576 (tp30) cc_final: 0.8361 (tp30) REVERT: I 195 ASP cc_start: 0.8930 (m-30) cc_final: 0.8704 (m-30) REVERT: P 48 ARG cc_start: 0.5940 (tpp80) cc_final: 0.5730 (tpp80) REVERT: P 76 MET cc_start: 0.8677 (ppp) cc_final: 0.8145 (ppp) REVERT: P 201 ILE cc_start: 0.9135 (mt) cc_final: 0.8857 (tp) REVERT: P 233 PHE cc_start: 0.7539 (m-80) cc_final: 0.7240 (m-80) REVERT: P 335 LEU cc_start: 0.8802 (mm) cc_final: 0.8597 (mp) REVERT: P 345 LEU cc_start: 0.8486 (tt) cc_final: 0.8009 (mp) REVERT: P 347 LEU cc_start: 0.8791 (mp) cc_final: 0.8583 (mp) REVERT: P 348 LYS cc_start: 0.8016 (mmtm) cc_final: 0.6702 (mmtp) REVERT: Q 85 ASN cc_start: 0.9297 (p0) cc_final: 0.8860 (p0) REVERT: Q 86 ASN cc_start: 0.8724 (m-40) cc_final: 0.8328 (m-40) REVERT: Q 112 MET cc_start: 0.8348 (mmm) cc_final: 0.7309 (mmm) REVERT: Q 114 TRP cc_start: 0.8103 (m-10) cc_final: 0.7726 (m-10) REVERT: Q 126 LEU cc_start: 0.9001 (tp) cc_final: 0.8642 (tt) REVERT: Q 137 PHE cc_start: 0.8788 (t80) cc_final: 0.8210 (t80) REVERT: Q 140 LYS cc_start: 0.9156 (ptpp) cc_final: 0.8736 (ptmm) REVERT: Q 141 ASN cc_start: 0.8928 (m110) cc_final: 0.8240 (m110) REVERT: Q 156 LYS cc_start: 0.8389 (mmpt) cc_final: 0.7960 (mmmt) REVERT: S 66 TRP cc_start: 0.8403 (m100) cc_final: 0.7811 (m-10) REVERT: T 80 LYS cc_start: 0.8649 (tmmt) cc_final: 0.8183 (mptt) REVERT: T 113 LEU cc_start: 0.9129 (mm) cc_final: 0.8833 (mm) REVERT: T 122 MET cc_start: 0.8316 (ptp) cc_final: 0.7497 (ppp) REVERT: T 133 ILE cc_start: 0.8825 (pt) cc_final: 0.8443 (pt) REVERT: W 43 TYR cc_start: 0.8919 (t80) cc_final: 0.8683 (t80) REVERT: W 45 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8692 (mm-30) REVERT: W 78 ASP cc_start: 0.8881 (t70) cc_final: 0.8616 (t70) REVERT: W 85 LEU cc_start: 0.9453 (mt) cc_final: 0.9201 (mt) REVERT: W 95 GLU cc_start: 0.8486 (tp30) cc_final: 0.8234 (tp30) REVERT: W 107 MET cc_start: 0.8807 (mmt) cc_final: 0.8264 (mmm) REVERT: W 127 MET cc_start: 0.7542 (tpp) cc_final: 0.7298 (mmm) REVERT: X 82 PHE cc_start: 0.9008 (t80) cc_final: 0.8609 (t80) REVERT: Z 10 MET cc_start: 0.8585 (mmm) cc_final: 0.7958 (mmt) REVERT: Z 72 MET cc_start: 0.9254 (mmt) cc_final: 0.8974 (mmt) REVERT: Z 75 PHE cc_start: 0.9160 (m-80) cc_final: 0.8714 (m-80) REVERT: a 12 MET cc_start: 0.9134 (ttm) cc_final: 0.8727 (tpp) REVERT: q 91 HIS cc_start: 0.8425 (m-70) cc_final: 0.8196 (m90) REVERT: q 127 TYR cc_start: 0.8911 (p90) cc_final: 0.8149 (p90) REVERT: q 142 THR cc_start: 0.8112 (t) cc_final: 0.7878 (m) REVERT: r 93 LYS cc_start: 0.8431 (mppt) cc_final: 0.7809 (mmmt) REVERT: s 57 LEU cc_start: 0.8581 (mm) cc_final: 0.8032 (pt) outliers start: 1 outliers final: 0 residues processed: 842 average time/residue: 0.1676 time to fit residues: 231.7507 Evaluate side-chains 662 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 662 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 363 optimal weight: 2.9990 chunk 100 optimal weight: 0.0020 chunk 277 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 378 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 193 optimal weight: 0.0980 overall best weight: 2.2194 ------------------------------------------------------------------------------- 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 166 ASN ** 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 190 HIS E 58 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 ASN Q 51 GLN ** Q 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 30 HIS ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.079823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.064171 restraints weight = 182763.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.066040 restraints weight = 118132.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.067379 restraints weight = 86732.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068357 restraints weight = 69175.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.069055 restraints weight = 58474.443| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.7716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34578 Z= 0.159 Angle : 0.972 81.183 46909 Z= 0.374 Chirality : 0.046 0.264 5135 Planarity : 0.005 0.060 5952 Dihedral : 7.462 154.777 4761 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.46 % Favored : 95.52 % Rotamer: Outliers : 0.06 % Allowed : 0.33 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.13), residues: 4127 helix: 0.40 (0.12), residues: 1899 sheet: -0.95 (0.27), residues: 350 loop : -0.82 (0.15), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 51 TYR 0.030 0.002 TYR B 170 PHE 0.068 0.002 PHE C 197 TRP 0.069 0.002 TRP C 170 HIS 0.006 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00363 (34542) covalent geometry : angle 0.72820 (46822) SS BOND : bond 0.00354 ( 3) SS BOND : angle 1.49775 ( 6) hydrogen bonds : bond 0.04120 ( 1439) hydrogen bonds : angle 5.19944 ( 4155) metal coordination : bond 0.01845 ( 33) metal coordination : angle 15.50736 ( 81) ********************** 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 839 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 837 time to evaluate : 1.144 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: symmetry clash REVERT: A 88 MET cc_start: 0.9052 (tpp) cc_final: 0.8403 (tpt) REVERT: A 90 MET cc_start: 0.6526 (ptt) cc_final: 0.6284 (ptt) REVERT: A 92 PHE cc_start: 0.7953 (m-10) cc_final: 0.7708 (m-10) REVERT: A 94 LEU cc_start: 0.8605 (pp) cc_final: 0.8396 (pp) REVERT: A 95 VAL cc_start: 0.8433 (t) cc_final: 0.8207 (t) REVERT: A 98 LEU cc_start: 0.8692 (mm) cc_final: 0.8457 (tp) REVERT: B 129 ASP cc_start: 0.7865 (t0) cc_final: 0.7211 (t0) REVERT: B 131 MET cc_start: 0.8808 (tpt) cc_final: 0.8491 (tpt) REVERT: B 208 LEU cc_start: 0.9823 (tp) cc_final: 0.9514 (tt) REVERT: C 118 VAL cc_start: 0.9591 (t) cc_final: 0.9310 (m) REVERT: C 166 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8379 (mt-10) REVERT: C 176 PHE cc_start: 0.8523 (t80) cc_final: 0.8182 (t80) REVERT: C 230 ARG cc_start: 0.8178 (mpp-170) cc_final: 0.7690 (mtt90) REVERT: D 185 MET cc_start: 0.9107 (tpp) cc_final: 0.8877 (tpp) REVERT: D 197 MET cc_start: 0.9176 (pmm) cc_final: 0.8841 (pmm) REVERT: D 210 MET cc_start: 0.9214 (mtm) cc_final: 0.8755 (mtm) REVERT: D 251 PHE cc_start: 0.9117 (t80) cc_final: 0.8831 (t80) REVERT: D 286 TYR cc_start: 0.8482 (m-80) cc_final: 0.8270 (m-80) REVERT: D 336 GLU cc_start: 0.9304 (mm-30) cc_final: 0.9073 (mm-30) REVERT: D 377 SER cc_start: 0.9427 (m) cc_final: 0.9220 (t) REVERT: D 404 LYS cc_start: 0.9080 (mmtp) cc_final: 0.8796 (mmtp) REVERT: D 443 MET cc_start: 0.9157 (mmp) cc_final: 0.8669 (mmp) REVERT: D 456 ILE cc_start: 0.9110 (mm) cc_final: 0.8748 (pt) REVERT: E 89 ASN cc_start: 0.8796 (t0) cc_final: 0.8535 (t0) REVERT: E 167 LEU cc_start: 0.8938 (mm) cc_final: 0.8641 (mm) REVERT: E 184 MET cc_start: 0.8790 (ptt) cc_final: 0.8469 (ptt) REVERT: E 242 PHE cc_start: 0.7116 (p90) cc_final: 0.6414 (p90) REVERT: F 42 PHE cc_start: 0.8515 (t80) cc_final: 0.7495 (t80) REVERT: F 62 TRP cc_start: 0.7817 (t60) cc_final: 0.7596 (t60) REVERT: F 136 HIS cc_start: 0.8140 (m-70) cc_final: 0.7865 (m-70) REVERT: F 149 MET cc_start: 0.7290 (mmm) cc_final: 0.7015 (mmt) REVERT: F 161 GLU cc_start: 0.9268 (mp0) cc_final: 0.8882 (mp0) REVERT: F 262 PHE cc_start: 0.8616 (t80) cc_final: 0.8224 (t80) REVERT: G 66 HIS cc_start: 0.8525 (t70) cc_final: 0.7972 (t-90) REVERT: G 77 MET cc_start: 0.9077 (tpt) cc_final: 0.8767 (tpp) REVERT: G 218 LEU cc_start: 0.9237 (mt) cc_final: 0.8930 (mt) REVERT: G 349 GLU cc_start: 0.8448 (pm20) cc_final: 0.7944 (pm20) REVERT: G 354 LEU cc_start: 0.9814 (tp) cc_final: 0.9577 (tt) REVERT: G 387 LEU cc_start: 0.8654 (mt) cc_final: 0.8170 (mt) REVERT: G 579 MET cc_start: 0.9191 (tpp) cc_final: 0.8887 (tpt) REVERT: G 643 ARG cc_start: 0.9043 (mmt90) cc_final: 0.8146 (tmm-80) REVERT: H 53 MET cc_start: 0.9178 (ttt) cc_final: 0.8967 (ttt) REVERT: H 71 PHE cc_start: 0.7300 (t80) cc_final: 0.6985 (t80) REVERT: H 83 LEU cc_start: 0.9512 (mt) cc_final: 0.9205 (mt) REVERT: H 183 MET cc_start: 0.9318 (mtt) cc_final: 0.8778 (mtt) REVERT: H 192 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8221 (tm-30) REVERT: H 195 ARG cc_start: 0.9168 (mmp80) cc_final: 0.8057 (mmp-170) REVERT: H 225 MET cc_start: 0.9021 (tpp) cc_final: 0.8711 (tpp) REVERT: H 227 GLU cc_start: 0.9162 (tp30) cc_final: 0.8750 (tp30) REVERT: H 231 ILE cc_start: 0.9718 (mt) cc_final: 0.9477 (mt) REVERT: H 303 TRP cc_start: 0.8595 (t-100) cc_final: 0.8258 (t-100) REVERT: I 51 LYS cc_start: 0.8503 (pttt) cc_final: 0.8085 (mtmt) REVERT: I 72 MET cc_start: 0.8718 (mmp) cc_final: 0.8071 (mmp) REVERT: I 145 TYR cc_start: 0.8617 (t80) cc_final: 0.8407 (t80) REVERT: I 151 LYS cc_start: 0.9473 (mttm) cc_final: 0.9241 (mmtt) REVERT: I 195 ASP cc_start: 0.8897 (m-30) cc_final: 0.8661 (m-30) REVERT: P 76 MET cc_start: 0.8644 (ppp) cc_final: 0.8150 (ppp) REVERT: P 96 LEU cc_start: 0.9169 (tp) cc_final: 0.8947 (tp) REVERT: P 201 ILE cc_start: 0.9153 (mt) cc_final: 0.8882 (tp) REVERT: P 233 PHE cc_start: 0.7645 (m-80) cc_final: 0.7360 (m-80) REVERT: P 345 LEU cc_start: 0.8502 (tt) cc_final: 0.8030 (mp) REVERT: P 348 LYS cc_start: 0.8004 (mmtm) cc_final: 0.6697 (mmtp) REVERT: Q 85 ASN cc_start: 0.9369 (p0) cc_final: 0.8901 (p0) REVERT: Q 86 ASN cc_start: 0.8770 (m-40) cc_final: 0.8373 (m-40) REVERT: Q 101 PHE cc_start: 0.8362 (m-10) cc_final: 0.7849 (m-80) REVERT: Q 112 MET cc_start: 0.8424 (mmm) cc_final: 0.7443 (mmm) REVERT: Q 114 TRP cc_start: 0.8136 (m-10) cc_final: 0.7635 (m-10) REVERT: Q 126 LEU cc_start: 0.9015 (tp) cc_final: 0.8740 (tt) REVERT: Q 156 LYS cc_start: 0.8446 (mmpt) cc_final: 0.8168 (mmmt) REVERT: T 80 LYS cc_start: 0.8711 (tmmt) cc_final: 0.8262 (mptt) REVERT: T 113 LEU cc_start: 0.9155 (mm) cc_final: 0.8832 (mm) REVERT: T 123 GLU cc_start: 0.5819 (tt0) cc_final: 0.5591 (tt0) REVERT: V 85 GLU cc_start: 0.8942 (pm20) cc_final: 0.8679 (pm20) REVERT: W 78 ASP cc_start: 0.8902 (t70) cc_final: 0.8641 (t70) REVERT: W 85 LEU cc_start: 0.9441 (mt) cc_final: 0.9192 (mt) REVERT: W 95 GLU cc_start: 0.8484 (tp30) cc_final: 0.8265 (tp30) REVERT: W 97 ILE cc_start: 0.9305 (mm) cc_final: 0.8477 (mm) REVERT: W 107 MET cc_start: 0.8820 (mmt) cc_final: 0.8242 (mmm) REVERT: W 127 MET cc_start: 0.7552 (tpp) cc_final: 0.7299 (mmm) REVERT: Z 10 MET cc_start: 0.8681 (mmm) cc_final: 0.8049 (mmt) REVERT: Z 72 MET cc_start: 0.9273 (mmt) cc_final: 0.9020 (mmt) REVERT: Z 75 PHE cc_start: 0.9106 (m-80) cc_final: 0.8683 (m-80) REVERT: a 12 MET cc_start: 0.9176 (ttm) cc_final: 0.8724 (tpp) REVERT: q 91 HIS cc_start: 0.8458 (m-70) cc_final: 0.8179 (m90) REVERT: q 127 TYR cc_start: 0.9010 (p90) cc_final: 0.8253 (p90) REVERT: q 142 THR cc_start: 0.8212 (t) cc_final: 0.7985 (m) REVERT: r 93 LYS cc_start: 0.8386 (mppt) cc_final: 0.7821 (mmmt) REVERT: s 57 LEU cc_start: 0.8549 (mm) cc_final: 0.8030 (pt) outliers start: 2 outliers final: 1 residues processed: 839 average time/residue: 0.1744 time to fit residues: 240.3849 Evaluate side-chains 651 residues out of total 3626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 650 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 329 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 392 optimal weight: 50.0000 chunk 218 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 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 B 166 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** 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 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 292 ASN ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** Q 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 141 ASN R 67 GLN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.077209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061816 restraints weight = 184603.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.063592 restraints weight = 118211.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.064897 restraints weight = 86194.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.065845 restraints weight = 68471.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066485 restraints weight = 57939.315| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.8003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 34578 Z= 0.210 Angle : 1.026 85.075 46909 Z= 0.393 Chirality : 0.047 0.258 5135 Planarity : 0.006 0.066 5952 Dihedral : 7.560 155.801 4761 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.06 % Allowed : 0.25 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.13), residues: 4127 helix: 0.38 (0.12), residues: 1881 sheet: -1.10 (0.27), residues: 342 loop : -0.85 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG S 20 TYR 0.040 0.002 TYR B 170 PHE 0.045 0.002 PHE H 224 TRP 0.082 0.003 TRP H 185 HIS 0.013 0.001 HIS S 22 Details of bonding type rmsd covalent geometry : bond 0.00464 (34542) covalent geometry : angle 0.75430 (46822) SS BOND : bond 0.00288 ( 3) SS BOND : angle 1.26726 ( 6) hydrogen bonds : bond 0.04278 ( 1439) hydrogen bonds : angle 5.34979 ( 4155) metal coordination : bond 0.02812 ( 33) metal coordination : angle 16.74521 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7001.58 seconds wall clock time: 121 minutes 43.01 seconds (7303.01 seconds total)