Starting phenix.real_space_refine on Tue Aug 26 02:56:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6khi_9989/08_2025/6khi_9989.cif Found real_map, /net/cci-nas-00/data/ceres_data/6khi_9989/08_2025/6khi_9989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6khi_9989/08_2025/6khi_9989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6khi_9989/08_2025/6khi_9989.map" model { file = "/net/cci-nas-00/data/ceres_data/6khi_9989/08_2025/6khi_9989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6khi_9989/08_2025/6khi_9989.cif" } resolution = 3.0 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 14 7.16 5 P 6 5.49 5 S 184 5.16 5 C 21526 2.51 5 N 5162 2.21 5 O 5743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.02s 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: 32635 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2821 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Chain: "B" Number of atoms: 3724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3724 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 18, 'TRANS': 473} Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 971 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3897 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 26, 'TRANS': 477} Chain: "E" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 775 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain: "F" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 4945 Classifications: {'peptide': 641} Link IDs: {'PTRANS': 32, 'TRANS': 608} Chain breaks: 2 Chain: "G" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1278 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3177 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain: "I" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1537 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain: "J" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1307 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 11, 'TRANS': 148} Chain: "K" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1590 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 20, 'TRANS': 184} Chain: "L" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "N" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 11, 'TRANS': 136} Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "P" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 321 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 333 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "S" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 469 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "V" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 838 Classifications: {'peptide': 109} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "1" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 756 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 124 Unusual residues: {'DGD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'LHG': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "D" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'BCR': 2, 'SQD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'LHG': 3, 'LMG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 41 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'LHG': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22426 SG CYS I 103 51.247 147.432 125.066 1.00 26.51 S ATOM 22470 SG CYS I 109 46.922 151.988 124.714 1.00 32.39 S ATOM 22175 SG CYS I 73 46.055 146.638 121.137 1.00 29.12 S ATOM 22451 SG CYS I 106 50.504 150.648 119.533 1.00 28.97 S ATOM 22122 SG CYS I 66 36.063 154.706 125.280 1.00 42.91 S ATOM 22144 SG CYS I 69 40.935 150.705 125.903 1.00 35.01 S ATOM 22103 SG CYS I 63 38.256 153.294 131.116 1.00 46.30 S ATOM 22504 SG CYS I 113 41.754 156.985 127.101 1.00 38.42 S ATOM 25530 SG CYS K 148 57.799 145.760 118.845 1.00 30.02 S ATOM 24806 SG CYS K 53 62.990 142.480 120.310 1.00 30.13 S ATOM 24800 SG CYS K 52 61.997 143.616 114.451 1.00 33.10 S ATOM 25304 SG CYS K 117 57.766 139.725 117.520 1.00 26.14 S ATOM 31484 SG CYS 1 41 32.927 160.609 122.910 1.00 83.69 S ATOM 31515 SG CYS 1 46 30.656 158.601 125.006 1.00 81.81 S ATOM 31534 SG CYS 1 49 27.912 161.206 121.565 1.00 94.03 S ATOM 31764 SG CYS 1 79 29.354 164.549 121.962 1.00100.16 S Time building chain proxies: 6.32, per 1000 atoms: 0.19 Number of scatterers: 32635 At special positions: 0 Unit cell: (168.48, 203.84, 172.64, 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 14 26.01 S 184 16.00 P 6 15.00 O 5743 8.00 N 5162 7.00 C 21526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.17 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 1 101 " pdb="FE2 FES 1 101 " - pdb=" SG CYS 1 49 " pdb="FE1 FES 1 101 " - pdb=" SG CYS 1 41 " pdb="FE1 FES 1 101 " - pdb=" SG CYS 1 46 " pdb="FE2 FES 1 101 " - pdb=" SG CYS 1 79 " pdb=" SF4 I 202 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 103 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 73 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 106 " pdb=" SF4 I 203 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 63 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 69 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 113 " pdb=" SF4 K 301 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 52 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 117 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 53 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 148 " Number of angles added : 42 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7536 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 23 sheets defined 59.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 removed outlier: 3.657A pdb=" N SER A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 30 through 60 removed outlier: 4.228A pdb=" N MET A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 56 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 74 through 86 removed outlier: 4.062A pdb=" N LEU A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 113 Proline residue: A 109 - end of helix Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.644A pdb=" N GLY A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.668A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.593A pdb=" N GLN A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 removed outlier: 3.811A pdb=" N LEU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 276 removed outlier: 3.891A pdb=" N TYR A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 299 through 330 removed outlier: 3.643A pdb=" N TRP A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 removed outlier: 3.562A pdb=" N GLY A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 366 Processing helix chain 'B' and resid 15 through 35 removed outlier: 3.843A pdb=" N LEU B 21 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.889A pdb=" N ARG B 41 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 63 removed outlier: 3.711A pdb=" N ILE B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Proline residue: B 60 - end of helix removed outlier: 3.813A pdb=" N THR B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 98 Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.761A pdb=" N THR B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 128 removed outlier: 3.870A pdb=" N ILE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 151 removed outlier: 3.579A pdb=" N GLY B 151 " --> pdb=" O TYR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 188 removed outlier: 3.675A pdb=" N ILE B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 207 through 224 removed outlier: 3.666A pdb=" N PHE B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 removed outlier: 5.374A pdb=" N GLN B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 removed outlier: 3.696A pdb=" N GLU B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 264 removed outlier: 4.232A pdb=" N SER B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 291 Processing helix chain 'B' and resid 298 through 321 removed outlier: 3.588A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 354 removed outlier: 3.833A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 369 through 385 Processing helix chain 'B' and resid 389 through 404 removed outlier: 3.998A pdb=" N PHE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 434 removed outlier: 3.905A pdb=" N TYR B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.002A pdb=" N ASN B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.635A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLY B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 487 Processing helix chain 'C' and resid 18 through 43 removed outlier: 3.607A pdb=" N PHE C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 24 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Proline residue: C 33 - end of helix Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 73 through 97 removed outlier: 3.821A pdb=" N PHE C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 102 through 126 removed outlier: 3.560A pdb=" N PHE C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 19 removed outlier: 3.671A pdb=" N THR D 9 " --> pdb=" O PRO D 5 " (cutoff:3.500A) Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 31 through 57 removed outlier: 3.949A pdb=" N ARG D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 57 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 106 Processing helix chain 'D' and resid 112 through 133 removed outlier: 4.403A pdb=" N GLY D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 130 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 161 through 189 removed outlier: 3.785A pdb=" N GLY D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 176 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE D 179 " --> pdb=" O GLY D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 Processing helix chain 'D' and resid 209 through 226 removed outlier: 3.639A pdb=" N LEU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 243 through 251 removed outlier: 3.832A pdb=" N LEU D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 265 Processing helix chain 'D' and resid 270 through 297 removed outlier: 3.851A pdb=" N LYS D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 302 through 313 removed outlier: 3.534A pdb=" N ILE D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 323 Processing helix chain 'D' and resid 325 through 358 removed outlier: 4.166A pdb=" N GLY D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.125A pdb=" N LYS D 371 " --> pdb=" O GLY D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 387 Processing helix chain 'D' and resid 392 through 407 removed outlier: 4.363A pdb=" N VAL D 396 " --> pdb=" O MET D 392 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 442 removed outlier: 3.654A pdb=" N ARG D 416 " --> pdb=" O SER D 412 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) Proline residue: D 431 - end of helix removed outlier: 4.076A pdb=" N LEU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 480 Proline residue: D 473 - end of helix Processing helix chain 'D' and resid 481 through 483 No H-bonds generated for 'chain 'D' and resid 481 through 483' Processing helix chain 'D' and resid 484 through 499 removed outlier: 3.877A pdb=" N TYR D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ALA D 490 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR D 491 " --> pdb=" O ILE D 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 19 Processing helix chain 'E' and resid 26 through 52 removed outlier: 3.594A pdb=" N VAL E 30 " --> pdb=" O ASN E 26 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 88 removed outlier: 3.668A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 97 removed outlier: 3.798A pdb=" N ASN E 97 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 7 Processing helix chain 'F' and resid 9 through 28 Proline residue: F 15 - end of helix removed outlier: 3.535A pdb=" N VAL F 22 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 34 removed outlier: 3.645A pdb=" N SER F 34 " --> pdb=" O SER F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 64 removed outlier: 4.288A pdb=" N GLY F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR F 57 " --> pdb=" O GLY F 53 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN F 64 " --> pdb=" O TRP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 115 removed outlier: 3.969A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 121 through 140 removed outlier: 3.782A pdb=" N LEU F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 163 removed outlier: 4.304A pdb=" N TRP F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 200 removed outlier: 3.811A pdb=" N GLY F 185 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLY F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU F 191 " --> pdb=" O PHE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 217 removed outlier: 4.118A pdb=" N ASP F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 241 removed outlier: 4.120A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 251 through 256 removed outlier: 3.539A pdb=" N MET F 254 " --> pdb=" O PRO F 251 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY F 256 " --> pdb=" O ALA F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 264 Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'F' and resid 272 through 280 Processing helix chain 'F' and resid 280 through 285 Processing helix chain 'F' and resid 287 through 312 removed outlier: 3.900A pdb=" N ILE F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR F 311 " --> pdb=" O THR F 307 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 336 Processing helix chain 'F' and resid 338 through 349 Processing helix chain 'F' and resid 352 through 369 removed outlier: 3.885A pdb=" N LEU F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 384 Processing helix chain 'F' and resid 386 through 391 removed outlier: 4.302A pdb=" N TYR F 390 " --> pdb=" O GLY F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 403 removed outlier: 4.981A pdb=" N GLY F 401 " --> pdb=" O THR F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 428 removed outlier: 3.518A pdb=" N LYS F 417 " --> pdb=" O GLY F 413 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU F 419 " --> pdb=" O TRP F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 455 removed outlier: 4.208A pdb=" N LEU F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU F 437 " --> pdb=" O LEU F 433 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY F 440 " --> pdb=" O TRP F 436 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU F 455 " --> pdb=" O PHE F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 493 Proline residue: F 489 - end of helix Processing helix chain 'F' and resid 499 through 505 removed outlier: 3.541A pdb=" N PHE F 502 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR F 505 " --> pdb=" O PHE F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 515 removed outlier: 3.832A pdb=" N VAL F 513 " --> pdb=" O ASN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 556 removed outlier: 3.971A pdb=" N SER F 539 " --> pdb=" O ILE F 535 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY F 544 " --> pdb=" O SER F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 569 removed outlier: 3.927A pdb=" N ILE F 569 " --> pdb=" O ILE F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 578 Processing helix chain 'F' and resid 581 through 589 Processing helix chain 'F' and resid 590 through 620 removed outlier: 4.473A pdb=" N VAL F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP F 610 " --> pdb=" O TYR F 606 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR F 620 " --> pdb=" O THR F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 631 Processing helix chain 'F' and resid 634 through 655 removed outlier: 3.823A pdb=" N SER F 653 " --> pdb=" O PHE F 649 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 654 " --> pdb=" O VAL F 650 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 28 removed outlier: 3.945A pdb=" N THR G 11 " --> pdb=" O THR G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 53 removed outlier: 3.564A pdb=" N SER G 35 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 66 removed outlier: 3.521A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 77 Processing helix chain 'G' and resid 98 through 116 Processing helix chain 'G' and resid 130 through 141 removed outlier: 3.761A pdb=" N THR G 134 " --> pdb=" O ASP G 130 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 165 removed outlier: 3.970A pdb=" N SER G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 56 removed outlier: 3.704A pdb=" N GLU H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 64 Processing helix chain 'H' and resid 76 through 91 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 95 through 126 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 130 through 149 removed outlier: 3.694A pdb=" N ILE H 134 " --> pdb=" O PRO H 130 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU H 139 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR H 140 " --> pdb=" O ARG H 136 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA H 148 " --> pdb=" O LEU H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 171 No H-bonds generated for 'chain 'H' and resid 169 through 171' Processing helix chain 'H' and resid 172 through 192 Proline residue: H 185 - end of helix removed outlier: 3.784A pdb=" N ASP H 188 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG H 192 " --> pdb=" O ASP H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 205 Processing helix chain 'H' and resid 211 through 219 Processing helix chain 'H' and resid 221 through 225 removed outlier: 3.681A pdb=" N MET H 224 " --> pdb=" O SER H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 283 removed outlier: 3.551A pdb=" N VAL H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 298 Processing helix chain 'H' and resid 376 through 386 removed outlier: 4.279A pdb=" N ALA H 380 " --> pdb=" O ALA H 376 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP H 386 " --> pdb=" O LEU H 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 30 Processing helix chain 'I' and resid 40 through 44 Processing helix chain 'I' and resid 60 through 63 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 107 through 112 Processing helix chain 'I' and resid 130 through 133 Processing helix chain 'I' and resid 183 through 193 removed outlier: 3.856A pdb=" N SER I 193 " --> pdb=" O ASN I 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 55 Processing helix chain 'J' and resid 118 through 129 Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.629A pdb=" N GLN J 165 " --> pdb=" O TYR J 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 41 Processing helix chain 'K' and resid 52 through 62 removed outlier: 3.923A pdb=" N GLU K 56 " --> pdb=" O CYS K 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET K 60 " --> pdb=" O GLU K 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE K 61 " --> pdb=" O PHE K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 71 removed outlier: 3.666A pdb=" N PHE K 70 " --> pdb=" O PHE K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 81 Processing helix chain 'K' and resid 93 through 104 removed outlier: 4.264A pdb=" N ALA K 97 " --> pdb=" O LYS K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 120 Processing helix chain 'K' and resid 121 through 125 removed outlier: 3.611A pdb=" N SER K 125 " --> pdb=" O GLY K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 138 Processing helix chain 'K' and resid 151 through 167 Processing helix chain 'L' and resid 5 through 22 Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 40 through 54 removed outlier: 3.660A pdb=" N PHE L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 62 Processing helix chain 'L' and resid 63 through 65 No H-bonds generated for 'chain 'L' and resid 63 through 65' Processing helix chain 'M' and resid 44 through 60 Processing helix chain 'M' and resid 66 through 87 removed outlier: 3.617A pdb=" N LEU M 70 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 17 Processing helix chain 'N' and resid 30 through 39 Processing helix chain 'N' and resid 48 through 52 removed outlier: 3.509A pdb=" N GLY N 51 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 59 Processing helix chain 'N' and resid 82 through 90 removed outlier: 3.714A pdb=" N LEU N 88 " --> pdb=" O VAL N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 123 removed outlier: 3.634A pdb=" N LEU N 116 " --> pdb=" O GLU N 112 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 147 Processing helix chain 'P' and resid 6 through 27 removed outlier: 4.558A pdb=" N ILE P 10 " --> pdb=" O SER P 6 " (cutoff:3.500A) Proline residue: P 16 - end of helix removed outlier: 4.570A pdb=" N THR P 27 " --> pdb=" O LEU P 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 42 Processing helix chain 'V' and resid 44 through 51 removed outlier: 4.014A pdb=" N ILE V 48 " --> pdb=" O PHE V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 59 Processing helix chain 'V' and resid 125 through 140 removed outlier: 3.782A pdb=" N GLN V 140 " --> pdb=" O ARG V 136 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 34 removed outlier: 3.616A pdb=" N VAL 1 29 " --> pdb=" O TYR 1 25 " (cutoff:3.500A) Processing helix chain '1' and resid 67 through 72 removed outlier: 3.944A pdb=" N GLU 1 72 " --> pdb=" O ASP 1 68 " (cutoff:3.500A) Processing helix chain '1' and resid 94 through 98 Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AA2, first strand: chain 'D' and resid 65 through 68 removed outlier: 5.140A pdb=" N LEU D 66 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA D 84 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 71 through 73 Processing sheet with id=AA4, first strand: chain 'F' and resid 69 through 76 removed outlier: 5.571A pdb=" N THR F 70 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE F 89 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N MET F 72 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR F 87 " --> pdb=" O MET F 72 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLU F 74 " --> pdb=" O MET F 85 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N MET F 85 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 27 through 30 Processing sheet with id=AA6, first strand: chain 'H' and resid 159 through 160 Processing sheet with id=AA7, first strand: chain 'H' and resid 327 through 331 Processing sheet with id=AA8, first strand: chain 'I' and resid 56 through 58 Processing sheet with id=AA9, first strand: chain 'I' and resid 79 through 82 removed outlier: 4.379A pdb=" N ASP I 81 " --> pdb=" O HIS I 95 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N HIS I 95 " --> pdb=" O ASP I 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 30 through 31 removed outlier: 4.111A pdb=" N GLY J 30 " --> pdb=" O MET J 38 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU J 37 " --> pdb=" O ARG J 95 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LYS J 97 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE J 39 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE J 99 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL J 41 " --> pdb=" O PHE J 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 60 through 62 Processing sheet with id=AB3, first strand: chain 'J' and resid 107 through 108 removed outlier: 6.781A pdb=" N VAL J 107 " --> pdb=" O GLU J 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 83 through 86 removed outlier: 3.654A pdb=" N MET K 114 " --> pdb=" O THR K 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 186 through 187 Processing sheet with id=AB6, first strand: chain 'M' and resid 15 through 17 Processing sheet with id=AB7, first strand: chain 'N' and resid 19 through 22 Processing sheet with id=AB8, first strand: chain 'N' and resid 43 through 47 Processing sheet with id=AB9, first strand: chain 'N' and resid 63 through 64 removed outlier: 3.715A pdb=" N HIS N 63 " --> pdb=" O GLN N 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 59 through 62 removed outlier: 6.935A pdb=" N TYR O 47 " --> pdb=" O ILE O 43 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE O 43 " --> pdb=" O TYR O 47 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN O 49 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY O 38 " --> pdb=" O VAL O 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 86 through 90 removed outlier: 5.854A pdb=" N LYS S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE S 70 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA S 76 " --> pdb=" O GLN S 68 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 88 through 89 removed outlier: 3.890A pdb=" N ARG V 88 " --> pdb=" O VAL V 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '1' and resid 16 through 20 removed outlier: 3.805A pdb=" N THR 1 16 " --> pdb=" O LEU 1 8 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ILE 1 89 " --> pdb=" O LYS 1 5 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR 1 7 " --> pdb=" O ILE 1 89 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS 1 88 " --> pdb=" O LEU 1 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '1' and resid 58 through 59 1658 hydrogen bonds defined for protein. 4824 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: 6.18 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 13448 1.40 - 1.63: 19646 1.63 - 1.85: 315 1.85 - 2.07: 0 2.07 - 2.29: 40 Bond restraints: 33449 Sorted by residual: bond pdb=" C6 SQD L 101 " pdb=" S SQD L 101 " ideal model delta sigma weight residual 1.840 1.616 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C6 SQD D 601 " pdb=" S SQD D 601 " ideal model delta sigma weight residual 1.840 1.618 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C6 SQD C 201 " pdb=" S SQD C 201 " ideal model delta sigma weight residual 1.840 1.621 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C25 BCR D 602 " pdb=" C26 BCR D 602 " ideal model delta sigma weight residual 1.347 1.557 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C25 BCR D 603 " pdb=" C26 BCR D 603 " ideal model delta sigma weight residual 1.347 1.554 -0.207 2.00e-02 2.50e+03 1.08e+02 ... (remaining 33444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.56: 45312 7.56 - 15.12: 129 15.12 - 22.68: 7 22.68 - 30.24: 6 30.24 - 37.80: 6 Bond angle restraints: 45460 Sorted by residual: angle pdb=" C6 SQD C 201 " pdb=" S SQD C 201 " pdb=" O7 SQD C 201 " ideal model delta sigma weight residual 111.32 73.52 37.80 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C6 SQD D 601 " pdb=" S SQD D 601 " pdb=" O7 SQD D 601 " ideal model delta sigma weight residual 111.32 73.66 37.66 3.00e+00 1.11e-01 1.58e+02 angle pdb=" S1 FES 1 101 " pdb="FE2 FES 1 101 " pdb=" S2 FES 1 101 " ideal model delta sigma weight residual 104.33 90.06 14.27 1.14e+00 7.69e-01 1.57e+02 angle pdb=" C6 SQD L 101 " pdb=" S SQD L 101 " pdb=" O7 SQD L 101 " ideal model delta sigma weight residual 111.32 73.99 37.33 3.00e+00 1.11e-01 1.55e+02 angle pdb=" S1 FES 1 101 " pdb="FE1 FES 1 101 " pdb=" S2 FES 1 101 " ideal model delta sigma weight residual 104.33 90.10 14.23 1.20e+00 6.94e-01 1.41e+02 ... (remaining 45455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 18334 24.77 - 49.53: 1202 49.53 - 74.30: 184 74.30 - 99.06: 33 99.06 - 123.83: 34 Dihedral angle restraints: 19787 sinusoidal: 8004 harmonic: 11783 Sorted by residual: dihedral pdb=" CA TYR H 72 " pdb=" C TYR H 72 " pdb=" N ALA H 73 " pdb=" CA ALA H 73 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASP H 71 " pdb=" C ASP H 71 " pdb=" N TYR H 72 " pdb=" CA TYR H 72 " ideal model delta harmonic sigma weight residual -180.00 -152.29 -27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA PRO I 164 " pdb=" C PRO I 164 " pdb=" N ALA I 165 " pdb=" CA ALA I 165 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 19784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.933: 5208 0.933 - 1.867: 0 1.867 - 2.800: 0 2.800 - 3.734: 0 3.734 - 4.667: 1 Chirality restraints: 5209 Sorted by residual: chirality pdb=" C1 SQD D 601 " pdb=" C2 SQD D 601 " pdb=" O5 SQD D 601 " pdb=" O6 SQD D 601 " both_signs ideal model delta sigma weight residual False -2.39 2.28 -4.67 2.00e-01 2.50e+01 5.45e+02 chirality pdb="FE1 SF4 K 301 " pdb=" S2 SF4 K 301 " pdb=" S3 SF4 K 301 " pdb=" S4 SF4 K 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" CB ILE H 154 " pdb=" CA ILE H 154 " pdb=" CG1 ILE H 154 " pdb=" CG2 ILE H 154 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 5206 not shown) Planarity restraints: 5614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 BCR D 603 " -0.279 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C17 BCR D 603 " 0.558 2.00e-02 2.50e+03 pdb=" C18 BCR D 603 " -0.290 2.00e-02 2.50e+03 pdb=" C19 BCR D 603 " -0.028 2.00e-02 2.50e+03 pdb=" C36 BCR D 603 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR D 602 " 0.491 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C11 BCR D 602 " -0.243 2.00e-02 2.50e+03 pdb=" C34 BCR D 602 " 0.110 2.00e-02 2.50e+03 pdb=" C8 BCR D 602 " -0.047 2.00e-02 2.50e+03 pdb=" C9 BCR D 602 " -0.311 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 BCR D 602 " -0.135 2.00e-02 2.50e+03 2.61e-01 8.52e+02 pdb=" C13 BCR D 602 " 0.327 2.00e-02 2.50e+03 pdb=" C14 BCR D 602 " -0.419 2.00e-02 2.50e+03 pdb=" C15 BCR D 602 " 0.199 2.00e-02 2.50e+03 pdb=" C35 BCR D 602 " 0.028 2.00e-02 2.50e+03 ... (remaining 5611 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7950 2.79 - 3.31: 29966 3.31 - 3.84: 58494 3.84 - 4.37: 70257 4.37 - 4.90: 119088 Nonbonded interactions: 285755 Sorted by model distance: nonbonded pdb=" OH TYR C 75 " pdb=" O ALA E 75 " model vdw 2.257 3.040 nonbonded pdb=" O ALA B 39 " pdb=" OG1 THR B 43 " model vdw 2.276 3.040 nonbonded pdb=" O ALA D 322 " pdb=" OH TYR D 411 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASP H 359 " pdb=" OG SER H 391 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLN B 310 " pdb=" OH TYR B 332 " model vdw 2.290 3.040 ... (remaining 285750 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.070 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.520 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.008 0.224 33465 Z= 0.395 Angle : 1.302 53.143 45502 Z= 0.574 Chirality : 0.087 4.667 5209 Planarity : 0.012 0.309 5614 Dihedral : 17.454 123.826 12251 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.94 % Favored : 91.03 % Rotamer: Outliers : 0.27 % Allowed : 7.74 % Favored : 91.99 % 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: -4.35 (0.10), residues: 4049 helix: -2.51 (0.08), residues: 2285 sheet: -2.96 (0.34), residues: 168 loop : -3.28 (0.13), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 277 TYR 0.034 0.002 TYR A 245 PHE 0.033 0.002 PHE A 321 TRP 0.027 0.002 TRP B 274 HIS 0.010 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00830 (33449) covalent geometry : angle 1.25087 (45460) hydrogen bonds : bond 0.14305 ( 1658) hydrogen bonds : angle 6.69772 ( 4824) metal coordination : bond 0.02023 ( 16) metal coordination : angle 11.90827 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 592 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 291 MET cc_start: 0.8769 (mmm) cc_final: 0.8343 (mmt) REVERT: G 95 LEU cc_start: 0.8151 (mt) cc_final: 0.7769 (OUTLIER) REVERT: H 22 MET cc_start: 0.6152 (mtp) cc_final: 0.5933 (tmt) REVERT: H 71 ASP cc_start: 0.5282 (p0) cc_final: 0.5080 (p0) REVERT: K 144 TYR cc_start: 0.8717 (m-80) cc_final: 0.8501 (m-80) REVERT: N 106 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7883 (mtmt) REVERT: 1 93 GLN cc_start: 0.7363 (mm110) cc_final: 0.6927 (mm-40) REVERT: 1 96 GLU cc_start: 0.7827 (mp0) cc_final: 0.7270 (mp0) outliers start: 9 outliers final: 5 residues processed: 600 average time/residue: 0.6142 time to fit residues: 436.7336 Evaluate side-chains 394 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 390 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain Q residue 9 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 0.0870 chunk 244 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 199 GLN A 339 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS B 296 GLN B 340 ASN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS E 2 GLN F 265 HIS F 313 ASN F 349 HIS F 570 GLN G 62 GLN G 71 ASN H 48 HIS H 156 ASN H 205 GLN I 6 GLN I 57 HIS J 135 HIS K 80 GLN K 181 HIS L 70 GLN M 9 HIS N 90 ASN S 64 GLN V 49 ASN V 86 GLN 1 70 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.100374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.084518 restraints weight = 72924.392| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.01 r_work: 0.3301 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33465 Z= 0.139 Angle : 0.784 39.218 45502 Z= 0.338 Chirality : 0.043 0.203 5209 Planarity : 0.005 0.076 5614 Dihedral : 13.103 108.199 5050 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.55 % Allowed : 14.95 % Favored : 82.50 % 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: -2.51 (0.12), residues: 4049 helix: -0.78 (0.10), residues: 2318 sheet: -2.84 (0.33), residues: 191 loop : -2.82 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 394 TYR 0.027 0.001 TYR L 31 PHE 0.028 0.001 PHE B 228 TRP 0.021 0.001 TRP B 274 HIS 0.005 0.001 HIS F 247 Details of bonding type rmsd covalent geometry : bond 0.00306 (33449) covalent geometry : angle 0.68238 (45460) hydrogen bonds : bond 0.04129 ( 1658) hydrogen bonds : angle 4.65507 ( 4824) metal coordination : bond 0.01331 ( 16) metal coordination : angle 12.70906 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 432 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.6853 (p0) REVERT: B 156 ASP cc_start: 0.8173 (t0) cc_final: 0.7969 (t70) REVERT: D 413 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7834 (tm) REVERT: F 193 MET cc_start: 0.8104 (ptm) cc_final: 0.7861 (ptm) REVERT: F 300 PHE cc_start: 0.8719 (t80) cc_final: 0.8497 (t80) REVERT: G 95 LEU cc_start: 0.8389 (mt) cc_final: 0.7833 (OUTLIER) REVERT: H 7 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7679 (mtp180) REVERT: H 22 MET cc_start: 0.6936 (mtp) cc_final: 0.5996 (tmt) REVERT: H 27 ARG cc_start: 0.9062 (mtm-85) cc_final: 0.8768 (mtm180) REVERT: H 57 ASN cc_start: 0.8458 (t0) cc_final: 0.8240 (t0) REVERT: H 202 ARG cc_start: 0.7329 (ptp-170) cc_final: 0.6847 (ptp-170) REVERT: H 224 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8163 (ttt) REVERT: J 100 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8663 (m) REVERT: K 27 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7690 (tp) REVERT: K 144 TYR cc_start: 0.9065 (m-80) cc_final: 0.8859 (m-80) REVERT: L 47 MET cc_start: 0.8560 (mmt) cc_final: 0.7838 (mtp) REVERT: N 89 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: Q 44 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.7005 (p90) REVERT: V 49 ASN cc_start: 0.7268 (m110) cc_final: 0.6992 (m110) REVERT: 1 4 TYR cc_start: 0.6886 (m-80) cc_final: 0.6573 (m-10) outliers start: 86 outliers final: 31 residues processed: 475 average time/residue: 0.5904 time to fit residues: 338.4895 Evaluate side-chains 429 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 392 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain 1 residue 18 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 123 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 265 optimal weight: 0.9980 chunk 325 optimal weight: 0.7980 chunk 313 optimal weight: 1.9990 chunk 336 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 447 ASN F 570 GLN F 574 GLN H 18 HIS H 84 ASN H 239 HIS S 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.082516 restraints weight = 70736.327| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.92 r_work: 0.3281 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33465 Z= 0.154 Angle : 0.760 39.265 45502 Z= 0.326 Chirality : 0.043 0.176 5209 Planarity : 0.005 0.073 5614 Dihedral : 11.354 108.283 5048 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 3.35 % Allowed : 16.97 % Favored : 79.68 % 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: -1.67 (0.13), residues: 4049 helix: -0.03 (0.11), residues: 2321 sheet: -2.80 (0.33), residues: 196 loop : -2.54 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 192 TYR 0.022 0.001 TYR A 245 PHE 0.022 0.001 PHE L 49 TRP 0.020 0.001 TRP B 274 HIS 0.005 0.001 HIS H 327 Details of bonding type rmsd covalent geometry : bond 0.00353 (33449) covalent geometry : angle 0.65316 (45460) hydrogen bonds : bond 0.03920 ( 1658) hydrogen bonds : angle 4.39939 ( 4824) metal coordination : bond 0.01475 ( 16) metal coordination : angle 12.77685 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 413 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.6841 (p0) REVERT: B 339 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8472 (ptt) REVERT: D 413 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7837 (tm) REVERT: E 89 ASP cc_start: 0.8094 (t70) cc_final: 0.7829 (t70) REVERT: G 95 LEU cc_start: 0.8373 (mt) cc_final: 0.7841 (pp) REVERT: H 22 MET cc_start: 0.6993 (mtp) cc_final: 0.6073 (tmt) REVERT: H 202 ARG cc_start: 0.7491 (ptp-170) cc_final: 0.7053 (ptp-170) REVERT: H 224 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8225 (ttt) REVERT: K 144 TYR cc_start: 0.9072 (m-80) cc_final: 0.8862 (m-80) REVERT: L 47 MET cc_start: 0.8557 (mmt) cc_final: 0.7894 (mtp) REVERT: L 66 ASN cc_start: 0.8512 (t0) cc_final: 0.8199 (t0) REVERT: M 59 ASN cc_start: 0.8863 (t0) cc_final: 0.8541 (m-40) REVERT: N 89 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: N 121 GLN cc_start: 0.8388 (mp10) cc_final: 0.7764 (mp10) REVERT: Q 44 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.7023 (p90) REVERT: V 49 ASN cc_start: 0.7229 (m110) cc_final: 0.6898 (m110) REVERT: 1 4 TYR cc_start: 0.6979 (m-80) cc_final: 0.6648 (m-10) REVERT: 1 5 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8471 (tmmm) outliers start: 113 outliers final: 43 residues processed: 481 average time/residue: 0.5977 time to fit residues: 348.1439 Evaluate side-chains 441 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 391 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 431 MET Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 80 GLN Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain 1 residue 5 LYS Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 18 ILE Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 322 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 374 optimal weight: 6.9990 chunk 271 optimal weight: 0.0010 chunk 387 optimal weight: 6.9990 chunk 299 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 319 optimal weight: 0.9990 chunk 265 optimal weight: 3.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 447 ASN K 170 HIS S 64 GLN 1 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080989 restraints weight = 70418.333| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.90 r_work: 0.3260 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33465 Z= 0.174 Angle : 0.769 42.500 45502 Z= 0.329 Chirality : 0.044 0.213 5209 Planarity : 0.005 0.073 5614 Dihedral : 10.192 108.312 5047 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.41 % Allowed : 18.24 % Favored : 78.34 % 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: -1.27 (0.13), residues: 4049 helix: 0.32 (0.11), residues: 2326 sheet: -2.79 (0.32), residues: 200 loop : -2.42 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 136 TYR 0.027 0.002 TYR L 31 PHE 0.022 0.001 PHE A 321 TRP 0.021 0.001 TRP B 274 HIS 0.005 0.001 HIS H 327 Details of bonding type rmsd covalent geometry : bond 0.00408 (33449) covalent geometry : angle 0.66074 (45460) hydrogen bonds : bond 0.03904 ( 1658) hydrogen bonds : angle 4.30273 ( 4824) metal coordination : bond 0.01533 ( 16) metal coordination : angle 12.96714 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 420 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.6804 (p0) REVERT: A 90 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8548 (tm) REVERT: A 186 MET cc_start: 0.8456 (mtp) cc_final: 0.8252 (mtp) REVERT: D 413 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7873 (tm) REVERT: D 437 MET cc_start: 0.8665 (ppp) cc_final: 0.8427 (ptm) REVERT: E 57 ILE cc_start: 0.8647 (mt) cc_final: 0.8390 (pt) REVERT: F 193 MET cc_start: 0.8176 (ptm) cc_final: 0.7858 (ptm) REVERT: F 381 MET cc_start: 0.7775 (mtm) cc_final: 0.7456 (mtm) REVERT: G 95 LEU cc_start: 0.8426 (mt) cc_final: 0.7889 (OUTLIER) REVERT: H 7 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7539 (mtp180) REVERT: H 22 MET cc_start: 0.6973 (mtp) cc_final: 0.6047 (tmt) REVERT: J 22 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6694 (pp30) REVERT: J 51 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8078 (tp-100) REVERT: J 100 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8722 (m) REVERT: L 47 MET cc_start: 0.8539 (mmt) cc_final: 0.7978 (mtp) REVERT: L 66 ASN cc_start: 0.8496 (t0) cc_final: 0.8189 (t0) REVERT: M 59 ASN cc_start: 0.8868 (t0) cc_final: 0.8566 (m110) REVERT: M 78 GLU cc_start: 0.7606 (tp30) cc_final: 0.7335 (mm-30) REVERT: N 89 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: N 121 GLN cc_start: 0.8423 (mp10) cc_final: 0.7821 (mp10) REVERT: Q 44 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.7050 (p90) REVERT: V 49 ASN cc_start: 0.7404 (m110) cc_final: 0.7046 (m110) REVERT: V 118 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8760 (pp) REVERT: V 128 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8504 (tp) REVERT: 1 1 MET cc_start: 0.4776 (OUTLIER) cc_final: 0.3777 (tmm) REVERT: 1 4 TYR cc_start: 0.6994 (m-80) cc_final: 0.6719 (m-10) REVERT: 1 28 ASP cc_start: 0.7689 (t0) cc_final: 0.7410 (m-30) REVERT: 1 69 ASP cc_start: 0.7695 (m-30) cc_final: 0.7454 (m-30) outliers start: 115 outliers final: 52 residues processed: 496 average time/residue: 0.5382 time to fit residues: 326.4589 Evaluate side-chains 440 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 379 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 80 GLN Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 118 LEU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 159 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 0.0060 chunk 299 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 365 optimal weight: 0.0020 chunk 349 optimal weight: 0.8980 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN D 232 HIS ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN G 97 GLN I 178 GLN M 16 HIS S 64 GLN V 135 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.099005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.083613 restraints weight = 70274.345| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.90 r_work: 0.3305 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33465 Z= 0.123 Angle : 0.738 43.962 45502 Z= 0.314 Chirality : 0.042 0.183 5209 Planarity : 0.005 0.070 5614 Dihedral : 9.741 106.886 5045 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.47 % Allowed : 18.84 % Favored : 77.69 % 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: -0.96 (0.13), residues: 4049 helix: 0.60 (0.11), residues: 2313 sheet: -2.78 (0.32), residues: 202 loop : -2.30 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 192 TYR 0.023 0.001 TYR K 48 PHE 0.021 0.001 PHE 1 39 TRP 0.022 0.001 TRP D 107 HIS 0.004 0.001 HIS D 247 Details of bonding type rmsd covalent geometry : bond 0.00274 (33449) covalent geometry : angle 0.62845 (45460) hydrogen bonds : bond 0.03617 ( 1658) hydrogen bonds : angle 4.18994 ( 4824) metal coordination : bond 0.01078 ( 16) metal coordination : angle 12.76331 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 419 time to evaluate : 1.482 Fit side-chains REVERT: A 23 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.6835 (p0) REVERT: D 321 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8110 (tp) REVERT: D 413 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7825 (tm) REVERT: E 57 ILE cc_start: 0.8512 (mt) cc_final: 0.8211 (pt) REVERT: E 100 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8245 (mtpt) REVERT: F 411 PHE cc_start: 0.8127 (m-10) cc_final: 0.7924 (m-10) REVERT: H 3 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6351 (pptt) REVERT: H 22 MET cc_start: 0.6943 (mtp) cc_final: 0.6044 (tmt) REVERT: I 87 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7129 (pm20) REVERT: J 22 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6713 (pp30) REVERT: J 100 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8734 (m) REVERT: K 190 MET cc_start: 0.8627 (mtt) cc_final: 0.8300 (mtp) REVERT: L 47 MET cc_start: 0.8514 (mmt) cc_final: 0.7979 (mtp) REVERT: L 66 ASN cc_start: 0.8437 (t0) cc_final: 0.8129 (t0) REVERT: M 27 GLU cc_start: 0.7556 (tp30) cc_final: 0.7326 (tp30) REVERT: M 55 GLU cc_start: 0.8598 (tt0) cc_final: 0.8298 (tt0) REVERT: M 59 ASN cc_start: 0.8853 (t0) cc_final: 0.8572 (m110) REVERT: M 78 GLU cc_start: 0.7470 (tp30) cc_final: 0.7202 (mm-30) REVERT: N 121 GLN cc_start: 0.8397 (mp10) cc_final: 0.7780 (mp10) REVERT: Q 44 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6986 (p90) REVERT: V 49 ASN cc_start: 0.7413 (m110) cc_final: 0.7048 (m110) REVERT: V 121 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7722 (pp20) REVERT: 1 1 MET cc_start: 0.4657 (OUTLIER) cc_final: 0.3832 (tmm) REVERT: 1 4 TYR cc_start: 0.6915 (m-80) cc_final: 0.6624 (m-10) REVERT: 1 5 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8493 (ttpp) outliers start: 117 outliers final: 47 residues processed: 495 average time/residue: 0.5743 time to fit residues: 345.1122 Evaluate side-chains 449 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 391 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 5 LYS Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 327 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 318 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 51 optimal weight: 6.9990 chunk 311 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN G 97 GLN ** H 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 HIS S 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.099673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.083421 restraints weight = 72622.340| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.00 r_work: 0.3271 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33465 Z= 0.154 Angle : 0.759 45.714 45502 Z= 0.324 Chirality : 0.043 0.207 5209 Planarity : 0.005 0.070 5614 Dihedral : 9.625 107.823 5045 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.06 % Allowed : 19.93 % Favored : 77.01 % 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: -0.83 (0.13), residues: 4049 helix: 0.70 (0.11), residues: 2315 sheet: -2.61 (0.34), residues: 194 loop : -2.26 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 192 TYR 0.020 0.001 TYR A 245 PHE 0.026 0.001 PHE F 131 TRP 0.027 0.001 TRP D 107 HIS 0.010 0.001 HIS D 247 Details of bonding type rmsd covalent geometry : bond 0.00360 (33449) covalent geometry : angle 0.65155 (45460) hydrogen bonds : bond 0.03707 ( 1658) hydrogen bonds : angle 4.19109 ( 4824) metal coordination : bond 0.01342 ( 16) metal coordination : angle 12.81537 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 398 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.6801 (p0) REVERT: B 58 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8308 (mtt) REVERT: D 250 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9146 (mp) REVERT: D 413 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7867 (tm) REVERT: E 57 ILE cc_start: 0.8589 (mt) cc_final: 0.8279 (pt) REVERT: E 100 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8299 (mtpt) REVERT: F 193 MET cc_start: 0.8169 (ptm) cc_final: 0.7837 (ptm) REVERT: F 411 PHE cc_start: 0.8140 (m-10) cc_final: 0.7912 (m-10) REVERT: H 22 MET cc_start: 0.7033 (mtp) cc_final: 0.6052 (tmt) REVERT: H 373 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7937 (mtm) REVERT: I 87 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: J 22 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6927 (pp30) REVERT: J 51 GLN cc_start: 0.8253 (mm-40) cc_final: 0.8019 (tp-100) REVERT: J 100 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8740 (m) REVERT: L 47 MET cc_start: 0.8609 (mmt) cc_final: 0.8183 (mtp) REVERT: L 66 ASN cc_start: 0.8477 (t0) cc_final: 0.8142 (t0) REVERT: M 59 ASN cc_start: 0.8920 (t0) cc_final: 0.8605 (m110) REVERT: M 78 GLU cc_start: 0.7548 (tp30) cc_final: 0.7270 (mm-30) REVERT: N 112 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7758 (mp0) REVERT: N 121 GLN cc_start: 0.8405 (mp10) cc_final: 0.7767 (mp10) REVERT: P 21 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8538 (mp) REVERT: Q 44 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.7017 (p90) REVERT: V 49 ASN cc_start: 0.7564 (m110) cc_final: 0.7194 (m110) REVERT: V 121 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7633 (pp20) REVERT: V 128 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8491 (tp) REVERT: 1 1 MET cc_start: 0.4693 (OUTLIER) cc_final: 0.3842 (tmm) REVERT: 1 4 TYR cc_start: 0.6918 (m-80) cc_final: 0.6643 (m-10) REVERT: 1 23 ASP cc_start: 0.6937 (m-30) cc_final: 0.6404 (m-30) REVERT: 1 28 ASP cc_start: 0.7841 (t0) cc_final: 0.7512 (m-30) REVERT: 1 69 ASP cc_start: 0.7651 (m-30) cc_final: 0.7335 (m-30) outliers start: 103 outliers final: 51 residues processed: 464 average time/residue: 0.5650 time to fit residues: 320.4907 Evaluate side-chains 456 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 392 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain S residue 52 LYS Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 67 optimal weight: 0.8980 chunk 229 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 303 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 350 optimal weight: 7.9990 chunk 213 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN G 97 GLN H 217 ASN S 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.096854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.081167 restraints weight = 71301.023| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.91 r_work: 0.3246 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33465 Z= 0.188 Angle : 0.785 47.227 45502 Z= 0.338 Chirality : 0.045 0.219 5209 Planarity : 0.005 0.071 5614 Dihedral : 9.660 108.590 5045 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.47 % Allowed : 20.02 % Favored : 76.51 % 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: -0.76 (0.14), residues: 4049 helix: 0.74 (0.11), residues: 2305 sheet: -2.54 (0.34), residues: 193 loop : -2.18 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 192 TYR 0.023 0.002 TYR K 48 PHE 0.028 0.001 PHE F 131 TRP 0.029 0.001 TRP D 107 HIS 0.006 0.001 HIS D 247 Details of bonding type rmsd covalent geometry : bond 0.00444 (33449) covalent geometry : angle 0.67728 (45460) hydrogen bonds : bond 0.03879 ( 1658) hydrogen bonds : angle 4.25145 ( 4824) metal coordination : bond 0.01556 ( 16) metal coordination : angle 13.06195 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 398 time to evaluate : 1.226 Fit side-chains REVERT: A 23 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.6813 (p0) REVERT: A 90 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8728 (tm) REVERT: B 58 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8304 (mtt) REVERT: D 250 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9170 (mp) REVERT: D 413 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7848 (tm) REVERT: E 100 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8338 (mtpt) REVERT: F 193 MET cc_start: 0.8240 (ptm) cc_final: 0.7880 (ptm) REVERT: H 22 MET cc_start: 0.7184 (mtp) cc_final: 0.6365 (tmt) REVERT: I 87 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: J 22 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6628 (pp30) REVERT: J 51 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8094 (tp-100) REVERT: J 100 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8728 (m) REVERT: K 27 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7576 (tp) REVERT: K 67 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7581 (t80) REVERT: L 47 MET cc_start: 0.8749 (mmt) cc_final: 0.8168 (mtp) REVERT: L 66 ASN cc_start: 0.8484 (t0) cc_final: 0.8168 (t0) REVERT: N 112 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7671 (mp0) REVERT: N 121 GLN cc_start: 0.8466 (mp10) cc_final: 0.7799 (mp10) REVERT: P 21 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8482 (mp) REVERT: Q 44 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.7061 (p90) REVERT: V 49 ASN cc_start: 0.7576 (m110) cc_final: 0.7233 (m110) REVERT: V 84 MET cc_start: 0.7843 (mmm) cc_final: 0.7195 (tmm) REVERT: V 121 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7655 (pp20) REVERT: V 128 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8545 (tp) REVERT: 1 1 MET cc_start: 0.4740 (OUTLIER) cc_final: 0.3872 (tmm) REVERT: 1 4 TYR cc_start: 0.6995 (m-80) cc_final: 0.6688 (m-10) REVERT: 1 5 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8416 (tmmt) REVERT: 1 23 ASP cc_start: 0.6943 (m-30) cc_final: 0.6389 (m-30) REVERT: 1 25 TYR cc_start: 0.8470 (m-80) cc_final: 0.8196 (m-80) REVERT: 1 28 ASP cc_start: 0.7861 (t0) cc_final: 0.7548 (m-30) REVERT: 1 69 ASP cc_start: 0.7641 (m-30) cc_final: 0.7268 (m-30) REVERT: 1 80 VAL cc_start: 0.9110 (m) cc_final: 0.8864 (m) outliers start: 117 outliers final: 58 residues processed: 477 average time/residue: 0.5692 time to fit residues: 331.8610 Evaluate side-chains 457 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 383 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 5 LYS Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 106 optimal weight: 1.9990 chunk 394 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 197 optimal weight: 0.0170 chunk 343 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 175 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 275 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN F 62 GLN G 97 GLN S 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.099485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.083121 restraints weight = 72184.539| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.00 r_work: 0.3282 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 33465 Z= 0.132 Angle : 0.785 47.606 45502 Z= 0.325 Chirality : 0.043 0.243 5209 Planarity : 0.005 0.166 5614 Dihedral : 9.457 107.758 5045 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.00 % Allowed : 21.00 % Favored : 76.00 % 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: -0.64 (0.14), residues: 4049 helix: 0.85 (0.11), residues: 2310 sheet: -2.41 (0.35), residues: 189 loop : -2.17 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 192 TYR 0.029 0.001 TYR H 182 PHE 0.027 0.001 PHE F 131 TRP 0.021 0.001 TRP B 274 HIS 0.005 0.001 HIS D 247 Details of bonding type rmsd covalent geometry : bond 0.00301 (33449) covalent geometry : angle 0.65190 (45460) hydrogen bonds : bond 0.03673 ( 1658) hydrogen bonds : angle 4.19371 ( 4824) metal coordination : bond 0.01124 ( 16) metal coordination : angle 14.42163 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 408 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.6802 (p0) REVERT: D 413 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7826 (tm) REVERT: E 100 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8294 (mtpt) REVERT: F 45 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8546 (mmm) REVERT: F 193 MET cc_start: 0.8148 (ptm) cc_final: 0.7855 (ptm) REVERT: F 367 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8657 (mtp) REVERT: H 22 MET cc_start: 0.7087 (mtp) cc_final: 0.6128 (tmt) REVERT: H 188 ASP cc_start: 0.7916 (p0) cc_final: 0.7457 (p0) REVERT: H 373 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7472 (mtm) REVERT: I 87 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: J 51 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8071 (tp-100) REVERT: J 100 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8745 (m) REVERT: J 139 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8297 (ptpp) REVERT: K 27 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7515 (tp) REVERT: K 67 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7430 (t80) REVERT: K 190 MET cc_start: 0.8665 (mtt) cc_final: 0.8324 (mtp) REVERT: L 47 MET cc_start: 0.8741 (mmt) cc_final: 0.8135 (mtp) REVERT: L 66 ASN cc_start: 0.8448 (t0) cc_final: 0.8129 (t0) REVERT: M 59 ASN cc_start: 0.8954 (t0) cc_final: 0.8614 (m-40) REVERT: N 112 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7748 (mp0) REVERT: N 121 GLN cc_start: 0.8454 (mp10) cc_final: 0.7810 (mp10) REVERT: Q 44 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.7011 (p90) REVERT: S 94 GLU cc_start: 0.8751 (pt0) cc_final: 0.8450 (pm20) REVERT: V 49 ASN cc_start: 0.7608 (m110) cc_final: 0.7318 (m-40) REVERT: V 84 MET cc_start: 0.7804 (mmm) cc_final: 0.7122 (tmm) REVERT: V 128 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8595 (tp) REVERT: 1 1 MET cc_start: 0.4655 (OUTLIER) cc_final: 0.3900 (tmm) REVERT: 1 4 TYR cc_start: 0.7081 (m-80) cc_final: 0.6774 (m-10) REVERT: 1 23 ASP cc_start: 0.6742 (m-30) cc_final: 0.6262 (m-30) REVERT: 1 28 ASP cc_start: 0.7867 (t0) cc_final: 0.7549 (m-30) REVERT: 1 69 ASP cc_start: 0.7587 (m-30) cc_final: 0.7224 (m-30) outliers start: 101 outliers final: 53 residues processed: 481 average time/residue: 0.5587 time to fit residues: 329.1607 Evaluate side-chains 440 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 374 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 5 LYS Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 245 optimal weight: 0.7980 chunk 329 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 389 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 317 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 293 optimal weight: 8.9990 chunk 276 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN G 97 GLN S 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.082457 restraints weight = 69990.611| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.89 r_work: 0.3290 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 33465 Z= 0.140 Angle : 0.794 47.983 45502 Z= 0.330 Chirality : 0.043 0.262 5209 Planarity : 0.005 0.106 5614 Dihedral : 9.354 107.695 5045 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.79 % Allowed : 21.18 % Favored : 76.03 % 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: -0.56 (0.14), residues: 4049 helix: 0.91 (0.11), residues: 2305 sheet: -2.49 (0.36), residues: 172 loop : -2.12 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 192 TYR 0.026 0.001 TYR H 182 PHE 0.034 0.001 PHE F 131 TRP 0.027 0.001 TRP D 107 HIS 0.008 0.001 HIS K 188 Details of bonding type rmsd covalent geometry : bond 0.00325 (33449) covalent geometry : angle 0.66175 (45460) hydrogen bonds : bond 0.03642 ( 1658) hydrogen bonds : angle 4.17515 ( 4824) metal coordination : bond 0.01258 ( 16) metal coordination : angle 14.46927 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 398 time to evaluate : 1.332 Fit side-chains REVERT: A 23 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.6797 (p0) REVERT: B 95 ILE cc_start: 0.8953 (tt) cc_final: 0.8752 (tt) REVERT: B 466 MET cc_start: 0.8321 (mmm) cc_final: 0.7858 (mtp) REVERT: D 321 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8075 (tp) REVERT: D 413 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7816 (tm) REVERT: D 492 THR cc_start: 0.8550 (m) cc_final: 0.8285 (p) REVERT: E 100 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8298 (mtpt) REVERT: F 45 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8414 (mmm) REVERT: F 193 MET cc_start: 0.8116 (ptm) cc_final: 0.7834 (ptm) REVERT: F 399 LEU cc_start: 0.8673 (mt) cc_final: 0.8294 (mp) REVERT: F 431 MET cc_start: 0.8650 (ptt) cc_final: 0.8397 (ptt) REVERT: H 7 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7735 (mtp180) REVERT: H 22 MET cc_start: 0.7152 (mtp) cc_final: 0.6149 (tmt) REVERT: H 373 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7470 (mtm) REVERT: H 389 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8129 (mpp) REVERT: J 51 GLN cc_start: 0.8264 (mm-40) cc_final: 0.8008 (tp-100) REVERT: J 100 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8736 (m) REVERT: J 139 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8295 (ptpp) REVERT: K 27 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7484 (tp) REVERT: K 67 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7421 (t80) REVERT: K 190 MET cc_start: 0.8648 (mtt) cc_final: 0.8332 (mtp) REVERT: L 47 MET cc_start: 0.8696 (mmt) cc_final: 0.8116 (mtp) REVERT: L 66 ASN cc_start: 0.8425 (t0) cc_final: 0.8112 (t0) REVERT: M 55 GLU cc_start: 0.8550 (tt0) cc_final: 0.8282 (tt0) REVERT: M 59 ASN cc_start: 0.8992 (t0) cc_final: 0.8645 (m-40) REVERT: M 78 GLU cc_start: 0.7436 (tp30) cc_final: 0.7192 (mm-30) REVERT: N 112 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7645 (mp0) REVERT: N 121 GLN cc_start: 0.8432 (mp10) cc_final: 0.7795 (mp10) REVERT: P 21 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8498 (mp) REVERT: Q 44 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.7069 (p90) REVERT: S 43 MET cc_start: 0.8054 (ptp) cc_final: 0.7465 (tmm) REVERT: S 94 GLU cc_start: 0.8736 (pt0) cc_final: 0.8441 (pm20) REVERT: V 49 ASN cc_start: 0.7608 (m110) cc_final: 0.7311 (m-40) REVERT: V 84 MET cc_start: 0.7725 (mmm) cc_final: 0.7056 (tmm) REVERT: V 128 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8573 (tp) REVERT: 1 1 MET cc_start: 0.4598 (OUTLIER) cc_final: 0.3676 (tmm) REVERT: 1 4 TYR cc_start: 0.7102 (m-80) cc_final: 0.6770 (m-10) REVERT: 1 5 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8373 (tmmt) REVERT: 1 23 ASP cc_start: 0.6757 (m-30) cc_final: 0.6266 (m-30) REVERT: 1 28 ASP cc_start: 0.7864 (t0) cc_final: 0.7543 (m-30) REVERT: 1 69 ASP cc_start: 0.7568 (m-30) cc_final: 0.7239 (m-30) outliers start: 94 outliers final: 60 residues processed: 460 average time/residue: 0.5720 time to fit residues: 321.3362 Evaluate side-chains 458 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 383 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 118 LEU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 5 LYS Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 389 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 371 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 334 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 361 optimal weight: 2.9990 chunk 270 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN S 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.097902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.082215 restraints weight = 70714.506| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.92 r_work: 0.3280 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33465 Z= 0.152 Angle : 0.802 48.402 45502 Z= 0.334 Chirality : 0.044 0.273 5209 Planarity : 0.005 0.083 5614 Dihedral : 9.322 107.676 5045 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.67 % Allowed : 21.60 % Favored : 75.73 % 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: -0.56 (0.14), residues: 4049 helix: 0.91 (0.11), residues: 2310 sheet: -2.62 (0.39), residues: 152 loop : -2.13 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 192 TYR 0.026 0.001 TYR H 182 PHE 0.034 0.001 PHE F 131 TRP 0.033 0.001 TRP D 107 HIS 0.011 0.001 HIS K 188 Details of bonding type rmsd covalent geometry : bond 0.00358 (33449) covalent geometry : angle 0.67002 (45460) hydrogen bonds : bond 0.03682 ( 1658) hydrogen bonds : angle 4.18015 ( 4824) metal coordination : bond 0.01380 ( 16) metal coordination : angle 14.54249 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8098 Ramachandran restraints generated. 4049 Oldfield, 0 Emsley, 4049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 387 time to evaluate : 1.330 Fit side-chains REVERT: A 23 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.6819 (p0) REVERT: B 466 MET cc_start: 0.8320 (mmm) cc_final: 0.7849 (mtp) REVERT: C 108 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8512 (mt-10) REVERT: D 321 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8111 (tp) REVERT: D 413 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7841 (tm) REVERT: D 492 THR cc_start: 0.8560 (m) cc_final: 0.8288 (p) REVERT: D 498 ARG cc_start: 0.6816 (ttp80) cc_final: 0.6527 (ttp80) REVERT: E 100 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8305 (mtpt) REVERT: F 45 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8510 (mmm) REVERT: F 343 LEU cc_start: 0.8771 (mt) cc_final: 0.8451 (mt) REVERT: F 399 LEU cc_start: 0.8698 (mt) cc_final: 0.8326 (mp) REVERT: F 431 MET cc_start: 0.8715 (ptt) cc_final: 0.8497 (ptt) REVERT: H 7 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7683 (mtm180) REVERT: H 22 MET cc_start: 0.7060 (mtp) cc_final: 0.6262 (tmt) REVERT: J 38 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8420 (mpp) REVERT: J 51 GLN cc_start: 0.8301 (mm-40) cc_final: 0.8041 (tp-100) REVERT: J 100 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8774 (m) REVERT: J 139 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8305 (ptpp) REVERT: K 27 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7338 (tp) REVERT: K 67 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7431 (t80) REVERT: K 190 MET cc_start: 0.8688 (mtt) cc_final: 0.8360 (mtp) REVERT: L 47 MET cc_start: 0.8693 (mmt) cc_final: 0.8096 (mtp) REVERT: L 66 ASN cc_start: 0.8444 (t0) cc_final: 0.8131 (t0) REVERT: M 55 GLU cc_start: 0.8589 (tt0) cc_final: 0.8324 (tt0) REVERT: M 59 ASN cc_start: 0.9015 (t0) cc_final: 0.8643 (m-40) REVERT: M 78 GLU cc_start: 0.7466 (tp30) cc_final: 0.7192 (mm-30) REVERT: N 112 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7648 (mp0) REVERT: N 121 GLN cc_start: 0.8439 (mp10) cc_final: 0.7797 (mp10) REVERT: P 21 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8504 (mp) REVERT: Q 44 TYR cc_start: 0.7367 (OUTLIER) cc_final: 0.7044 (p90) REVERT: S 43 MET cc_start: 0.7998 (ptp) cc_final: 0.7413 (tmm) REVERT: S 94 GLU cc_start: 0.8757 (pt0) cc_final: 0.8456 (pm20) REVERT: V 49 ASN cc_start: 0.7728 (m110) cc_final: 0.7407 (m-40) REVERT: V 84 MET cc_start: 0.7707 (mmm) cc_final: 0.7095 (tmm) REVERT: V 128 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8530 (tp) REVERT: 1 1 MET cc_start: 0.4713 (OUTLIER) cc_final: 0.3871 (tmm) REVERT: 1 4 TYR cc_start: 0.7116 (m-80) cc_final: 0.6789 (m-10) REVERT: 1 8 LEU cc_start: 0.8800 (mm) cc_final: 0.8301 (mt) REVERT: 1 23 ASP cc_start: 0.6810 (m-30) cc_final: 0.6312 (m-30) REVERT: 1 28 ASP cc_start: 0.7868 (t0) cc_final: 0.7571 (m-30) outliers start: 90 outliers final: 59 residues processed: 445 average time/residue: 0.5763 time to fit residues: 313.7644 Evaluate side-chains 453 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 381 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 38 MET Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 118 LEU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 347 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 170 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 306 optimal weight: 0.9990 chunk 315 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 282 optimal weight: 0.5980 chunk 246 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 ASN G 97 GLN S 64 GLN 1 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.100415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.084148 restraints weight = 72583.206| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.01 r_work: 0.3284 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33465 Z= 0.132 Angle : 0.793 48.527 45502 Z= 0.329 Chirality : 0.043 0.261 5209 Planarity : 0.005 0.067 5614 Dihedral : 9.171 107.652 5045 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.55 % Allowed : 21.89 % Favored : 75.56 % 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: -0.48 (0.14), residues: 4049 helix: 0.99 (0.11), residues: 2301 sheet: -2.76 (0.37), residues: 167 loop : -2.06 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 192 TYR 0.035 0.001 TYR I 20 PHE 0.050 0.001 PHE V 44 TRP 0.026 0.001 TRP D 107 HIS 0.007 0.001 HIS K 188 Details of bonding type rmsd covalent geometry : bond 0.00303 (33449) covalent geometry : angle 0.65859 (45460) hydrogen bonds : bond 0.03565 ( 1658) hydrogen bonds : angle 4.14480 ( 4824) metal coordination : bond 0.01137 ( 16) metal coordination : angle 14.54500 ( 42) =============================================================================== Job complete usr+sys time: 12161.26 seconds wall clock time: 207 minutes 34.44 seconds (12454.44 seconds total)