Starting phenix.real_space_refine on Sat Jun 28 07:47:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6khi_9989/06_2025/6khi_9989.cif Found real_map, /net/cci-nas-00/data/ceres_data/6khi_9989/06_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_9989/06_2025/6khi_9989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6khi_9989/06_2025/6khi_9989.map" model { file = "/net/cci-nas-00/data/ceres_data/6khi_9989/06_2025/6khi_9989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6khi_9989/06_2025/6khi_9989.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.76, per 1000 atoms: 0.51 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: 8.60 Conformation dependent library (CDL) restraints added in 4.1 seconds 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: 2.92 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: 11.68 Time building geometry restraints manager: 9.97 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: 0.010 Normalize map: mean=0, sd=1: 4.460 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: 1.200 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 76.360 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.290 ------------------------------------------------------------------------------- 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 : 7.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.002 TRP B 274 HIS 0.010 0.001 HIS D 339 PHE 0.033 0.002 PHE A 321 TYR 0.034 0.002 TYR A 245 ARG 0.015 0.001 ARG H 277 Details of bonding type rmsd hydrogen bonds : bond 0.14305 ( 1658) hydrogen bonds : angle 6.69772 ( 4824) metal coordination : bond 0.02023 ( 16) metal coordination : angle 11.90827 ( 42) covalent geometry : bond 0.00830 (33449) covalent geometry : angle 1.25087 (45460) *********************** 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 : 3.377 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: 0.7759 (pp) 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: 0.5081 (p0) REVERT: K 144 TYR cc_start: 0.8717 (m-80) cc_final: 0.8502 (m-80) REVERT: N 106 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7884 (mtmt) REVERT: 1 93 GLN cc_start: 0.7363 (mm110) cc_final: 0.6929 (mm-40) REVERT: 1 96 GLU cc_start: 0.7827 (mp0) cc_final: 0.7268 (mp0) outliers start: 9 outliers final: 4 residues processed: 600 average time/residue: 1.7066 time to fit residues: 1214.3014 Evaluate side-chains 395 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 391 time to evaluate : 5.438 ------------------------------------------------------------------------------- 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 339 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 315 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 234 optimal weight: 0.8980 chunk 365 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN A 208 ASN 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 H 239 HIS I 6 GLN I 9 ASN 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.099792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.083644 restraints weight = 72727.220| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.03 r_work: 0.3282 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33465 Z= 0.151 Angle : 0.791 39.055 45502 Z= 0.340 Chirality : 0.043 0.206 5209 Planarity : 0.005 0.076 5614 Dihedral : 12.995 108.465 5050 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.70 % Allowed : 14.83 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.12), residues: 4049 helix: -0.78 (0.10), residues: 2317 sheet: -2.85 (0.33), residues: 191 loop : -2.80 (0.14), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 274 HIS 0.005 0.001 HIS H 327 PHE 0.026 0.001 PHE B 228 TYR 0.023 0.001 TYR L 31 ARG 0.007 0.001 ARG H 394 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 1658) hydrogen bonds : angle 4.65185 ( 4824) metal coordination : bond 0.01426 ( 16) metal coordination : angle 12.93258 ( 42) covalent geometry : bond 0.00338 (33449) covalent geometry : angle 0.68671 (45460) *********************** 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 524 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 433 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.6826 (p0) REVERT: D 413 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7879 (tm) REVERT: E 89 ASP cc_start: 0.8092 (t70) cc_final: 0.7807 (t70) REVERT: F 193 MET cc_start: 0.8155 (ptm) cc_final: 0.7916 (ptm) REVERT: F 300 PHE cc_start: 0.8728 (t80) cc_final: 0.8507 (t80) REVERT: F 411 PHE cc_start: 0.8311 (m-10) cc_final: 0.8107 (m-10) REVERT: G 95 LEU cc_start: 0.8403 (mt) cc_final: 0.7850 (OUTLIER) REVERT: H 7 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7685 (mtp180) REVERT: H 22 MET cc_start: 0.6988 (mtp) cc_final: 0.6045 (tmt) REVERT: H 202 ARG cc_start: 0.7329 (ptp-170) cc_final: 0.6854 (ptp-170) REVERT: H 224 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8174 (ttt) REVERT: J 100 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8669 (m) REVERT: K 27 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7695 (tp) REVERT: L 47 MET cc_start: 0.8500 (mmt) cc_final: 0.7681 (mtp) REVERT: M 27 GLU cc_start: 0.7648 (tp30) cc_final: 0.7443 (tp30) REVERT: N 89 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: Q 44 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6997 (p90) REVERT: V 49 ASN cc_start: 0.7291 (m110) cc_final: 0.7032 (m110) REVERT: 1 4 TYR cc_start: 0.6872 (m-80) cc_final: 0.6568 (m-10) REVERT: 1 70 GLN cc_start: 0.8502 (mt0) cc_final: 0.8293 (mt0) outliers start: 91 outliers final: 33 residues processed: 480 average time/residue: 1.4041 time to fit residues: 815.4425 Evaluate side-chains 425 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 386 time to evaluate : 3.688 ------------------------------------------------------------------------------- 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 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 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 E residue 91 VAL 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 Chi-restraints excluded: chain 1 residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 359 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 378 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 384 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 447 ASN F 570 GLN F 574 GLN H 18 HIS H 78 ASN H 84 ASN I 9 ASN ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN S 64 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.079392 restraints weight = 71126.451| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.91 r_work: 0.3232 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33465 Z= 0.220 Angle : 0.809 40.779 45502 Z= 0.350 Chirality : 0.045 0.187 5209 Planarity : 0.005 0.076 5614 Dihedral : 11.424 109.631 5048 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.62 % Allowed : 17.06 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 4049 helix: -0.09 (0.11), residues: 2324 sheet: -2.84 (0.32), residues: 211 loop : -2.52 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 107 HIS 0.006 0.001 HIS H 327 PHE 0.025 0.002 PHE A 321 TYR 0.023 0.002 TYR A 245 ARG 0.008 0.000 ARG H 192 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 1658) hydrogen bonds : angle 4.48341 ( 4824) metal coordination : bond 0.01986 ( 16) metal coordination : angle 13.45190 ( 42) covalent geometry : bond 0.00513 (33449) covalent geometry : angle 0.69897 (45460) *********************** 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 525 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 403 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8594 (tm) REVERT: B 58 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8464 (mtt) REVERT: D 413 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7902 (tm) REVERT: F 35 LYS cc_start: 0.8013 (mtmt) cc_final: 0.7712 (pttt) REVERT: F 300 PHE cc_start: 0.8677 (t80) cc_final: 0.8445 (t80) REVERT: F 367 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8797 (mmt) REVERT: F 411 PHE cc_start: 0.8487 (m-10) cc_final: 0.8257 (m-10) REVERT: H 22 MET cc_start: 0.7069 (mtp) cc_final: 0.6361 (tmt) REVERT: H 57 ASN cc_start: 0.8501 (t0) cc_final: 0.8259 (t0) REVERT: H 202 ARG cc_start: 0.7459 (ptp-170) cc_final: 0.7122 (ptp-170) REVERT: L 47 MET cc_start: 0.8569 (mmt) cc_final: 0.7951 (mtp) REVERT: M 59 ASN cc_start: 0.8972 (t0) cc_final: 0.8640 (m-40) REVERT: M 77 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9189 (tt) REVERT: N 121 GLN cc_start: 0.8406 (mp10) cc_final: 0.7999 (mp10) REVERT: Q 44 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.7066 (p90) REVERT: V 49 ASN cc_start: 0.7372 (m110) cc_final: 0.7060 (m110) REVERT: 1 4 TYR cc_start: 0.6937 (m-80) cc_final: 0.6582 (m-10) REVERT: 1 5 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8466 (tmmm) outliers start: 122 outliers final: 53 residues processed: 472 average time/residue: 1.3052 time to fit residues: 746.4250 Evaluate side-chains 437 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 377 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 49 ARG 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 378 MET 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 190 LEU Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 105 LEU 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 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 131 VAL Chi-restraints excluded: chain J residue 158 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 M residue 77 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 106 LYS Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 17 VAL 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 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 71 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 81 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 202 optimal weight: 0.9990 chunk 372 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 327 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 323 optimal weight: 0.7980 chunk 331 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 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 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN B 130 GLN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 447 ASN H 78 ASN I 9 ASN J 20 GLN K 170 HIS ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN 1 93 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.096274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.080624 restraints weight = 70649.727| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.90 r_work: 0.3280 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33465 Z= 0.136 Angle : 0.756 43.679 45502 Z= 0.320 Chirality : 0.043 0.203 5209 Planarity : 0.005 0.073 5614 Dihedral : 10.236 107.442 5045 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.20 % Allowed : 18.60 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 4049 helix: 0.34 (0.11), residues: 2320 sheet: -2.82 (0.32), residues: 200 loop : -2.40 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 274 HIS 0.004 0.001 HIS D 339 PHE 0.019 0.001 PHE L 49 TYR 0.022 0.001 TYR L 31 ARG 0.009 0.000 ARG H 192 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 1658) hydrogen bonds : angle 4.30339 ( 4824) metal coordination : bond 0.01260 ( 16) metal coordination : angle 13.11749 ( 42) covalent geometry : bond 0.00308 (33449) covalent geometry : angle 0.64227 (45460) *********************** 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 526 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 418 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.6790 (p0) REVERT: A 186 MET cc_start: 0.8413 (mtp) cc_final: 0.8154 (mtp) REVERT: A 276 TYR cc_start: 0.8603 (m-80) cc_final: 0.8384 (m-80) REVERT: D 250 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9091 (mp) REVERT: D 413 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7854 (tm) REVERT: D 437 MET cc_start: 0.8619 (ppp) cc_final: 0.8370 (ptm) REVERT: E 57 ILE cc_start: 0.8610 (mt) cc_final: 0.8350 (pt) REVERT: E 100 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8319 (mtpt) REVERT: F 35 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7750 (pttt) REVERT: F 300 PHE cc_start: 0.8637 (t80) cc_final: 0.8401 (t80) REVERT: F 381 MET cc_start: 0.7587 (mtm) cc_final: 0.7356 (mtm) REVERT: F 411 PHE cc_start: 0.8334 (m-10) cc_final: 0.8100 (m-10) REVERT: H 22 MET cc_start: 0.7024 (mtp) cc_final: 0.6082 (tmt) REVERT: H 57 ASN cc_start: 0.8533 (t0) cc_final: 0.8257 (t0) REVERT: H 132 PHE cc_start: 0.7391 (m-80) cc_final: 0.7154 (m-80) REVERT: J 22 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6708 (pp30) REVERT: J 100 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8723 (m) REVERT: K 67 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7296 (t80) REVERT: L 47 MET cc_start: 0.8543 (mmt) cc_final: 0.8013 (mtp) REVERT: L 66 ASN cc_start: 0.8484 (t0) cc_final: 0.8172 (t0) REVERT: M 27 GLU cc_start: 0.7675 (tp30) cc_final: 0.7458 (tp30) REVERT: M 59 ASN cc_start: 0.8879 (t0) cc_final: 0.8583 (m110) REVERT: N 89 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: N 121 GLN cc_start: 0.8417 (mp10) cc_final: 0.7777 (mp10) REVERT: Q 44 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6998 (p90) REVERT: V 49 ASN cc_start: 0.7429 (m110) cc_final: 0.7063 (m110) REVERT: V 128 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8510 (tp) REVERT: 1 1 MET cc_start: 0.4384 (OUTLIER) cc_final: 0.3379 (tmm) REVERT: 1 4 TYR cc_start: 0.7000 (m-80) cc_final: 0.6676 (m-10) REVERT: 1 39 PHE cc_start: 0.8942 (p90) cc_final: 0.8725 (p90) outliers start: 108 outliers final: 43 residues processed: 486 average time/residue: 1.2847 time to fit residues: 766.4758 Evaluate side-chains 432 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 379 time to evaluate : 3.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 28 ILE 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 250 LEU 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 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 129 THR Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 ILE 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 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 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 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 99 VAL Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 113 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 325 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 163 optimal weight: 0.4980 chunk 157 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 124 optimal weight: 0.1980 chunk 168 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 367 optimal weight: 3.9990 chunk 329 optimal weight: 20.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 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 447 ASN G 97 GLN I 9 ASN I 178 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 HIS S 64 GLN V 135 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.082639 restraints weight = 70034.037| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.91 r_work: 0.3287 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33465 Z= 0.131 Angle : 0.743 44.202 45502 Z= 0.316 Chirality : 0.043 0.182 5209 Planarity : 0.005 0.071 5614 Dihedral : 9.790 107.698 5045 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.71 % Allowed : 18.87 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4049 helix: 0.58 (0.11), residues: 2316 sheet: -2.82 (0.32), residues: 202 loop : -2.28 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 274 HIS 0.004 0.001 HIS D 339 PHE 0.019 0.001 PHE A 321 TYR 0.020 0.001 TYR A 245 ARG 0.009 0.000 ARG H 192 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 1658) hydrogen bonds : angle 4.22114 ( 4824) metal coordination : bond 0.01190 ( 16) metal coordination : angle 12.90511 ( 42) covalent geometry : bond 0.00298 (33449) covalent geometry : angle 0.63156 (45460) *********************** 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 541 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 416 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.6832 (p0) REVERT: A 90 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8562 (tm) REVERT: B 6 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5855 (pp) REVERT: D 321 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8083 (tp) REVERT: D 413 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7841 (tm) REVERT: E 57 ILE cc_start: 0.8569 (mt) cc_final: 0.8274 (pt) REVERT: E 100 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8357 (mtpt) REVERT: F 193 MET cc_start: 0.8113 (ptm) cc_final: 0.7795 (ptm) REVERT: F 300 PHE cc_start: 0.8582 (t80) cc_final: 0.8319 (t80) REVERT: F 411 PHE cc_start: 0.8287 (m-10) cc_final: 0.8052 (m-10) REVERT: H 3 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6458 (pptt) REVERT: H 22 MET cc_start: 0.6903 (mtp) cc_final: 0.6015 (tmt) REVERT: H 57 ASN cc_start: 0.8537 (t0) cc_final: 0.8301 (t0) REVERT: H 132 PHE cc_start: 0.7399 (m-80) cc_final: 0.7159 (m-80) REVERT: I 87 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: J 22 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6687 (pp30) REVERT: J 51 GLN cc_start: 0.8339 (mm-40) cc_final: 0.8100 (tp-100) REVERT: J 81 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8462 (pp) REVERT: J 100 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8745 (m) REVERT: L 47 MET cc_start: 0.8494 (mmt) cc_final: 0.7942 (mtp) REVERT: L 66 ASN cc_start: 0.8465 (t0) cc_final: 0.8153 (t0) REVERT: M 59 ASN cc_start: 0.8851 (t0) cc_final: 0.8527 (m-40) REVERT: N 121 GLN cc_start: 0.8419 (mp10) cc_final: 0.7788 (mp10) REVERT: Q 44 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.7006 (p90) REVERT: V 49 ASN cc_start: 0.7514 (m110) cc_final: 0.7135 (m110) REVERT: V 121 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7663 (pp20) REVERT: V 128 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8495 (tp) REVERT: 1 1 MET cc_start: 0.4517 (OUTLIER) cc_final: 0.3461 (tmm) REVERT: 1 4 TYR cc_start: 0.6984 (m-80) cc_final: 0.6704 (m-10) REVERT: 1 23 ASP cc_start: 0.7328 (m-30) cc_final: 0.7081 (m-30) REVERT: 1 28 ASP cc_start: 0.7772 (t0) cc_final: 0.7453 (m-30) REVERT: 1 55 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: 1 69 ASP cc_start: 0.7616 (m-30) cc_final: 0.7379 (m-30) outliers start: 125 outliers final: 55 residues processed: 500 average time/residue: 1.2448 time to fit residues: 758.7244 Evaluate side-chains 461 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 391 time to evaluate : 3.563 ------------------------------------------------------------------------------- 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 6 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER 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 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 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 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 3 LYS 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 283 LEU Chi-restraints excluded: chain H residue 375 VAL 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 81 LEU 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 22 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 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 55 GLU 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 348 optimal weight: 1.9990 chunk 390 optimal weight: 6.9990 chunk 373 optimal weight: 0.0270 chunk 245 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 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 447 ASN G 97 GLN I 9 ASN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 HIS ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.099733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.083693 restraints weight = 72605.963| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.00 r_work: 0.3289 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33465 Z= 0.133 Angle : 0.748 46.483 45502 Z= 0.319 Chirality : 0.043 0.192 5209 Planarity : 0.005 0.070 5614 Dihedral : 9.615 107.597 5045 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.29 % Allowed : 20.14 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4049 helix: 0.72 (0.11), residues: 2312 sheet: -2.85 (0.32), residues: 202 loop : -2.21 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 107 HIS 0.010 0.001 HIS D 247 PHE 0.030 0.001 PHE F 131 TYR 0.027 0.001 TYR L 31 ARG 0.010 0.000 ARG H 192 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 1658) hydrogen bonds : angle 4.17967 ( 4824) metal coordination : bond 0.01185 ( 16) metal coordination : angle 12.92762 ( 42) covalent geometry : bond 0.00304 (33449) covalent geometry : angle 0.63714 (45460) *********************** 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 516 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 405 time to evaluate : 3.708 Fit side-chains REVERT: A 23 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.6845 (p0) REVERT: A 90 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8628 (tm) REVERT: B 6 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5609 (pp) REVERT: D 250 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9163 (mp) REVERT: D 321 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8090 (tp) REVERT: D 413 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7840 (tm) REVERT: E 57 ILE cc_start: 0.8546 (mt) cc_final: 0.8237 (pt) REVERT: E 100 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8328 (mtpt) REVERT: F 300 PHE cc_start: 0.8607 (t80) cc_final: 0.8348 (t80) REVERT: F 411 PHE cc_start: 0.8267 (m-10) cc_final: 0.8050 (m-10) REVERT: H 22 MET cc_start: 0.6970 (mtp) cc_final: 0.6004 (tmt) REVERT: H 57 ASN cc_start: 0.8578 (t0) cc_final: 0.8338 (t0) REVERT: H 340 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.9012 (mp) REVERT: H 373 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7942 (mtm) REVERT: I 87 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: J 22 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6869 (pp30) REVERT: J 100 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8733 (m) REVERT: K 190 MET cc_start: 0.8637 (mtt) cc_final: 0.8305 (mtp) REVERT: L 47 MET cc_start: 0.8529 (mmt) cc_final: 0.7960 (mtp) REVERT: L 66 ASN cc_start: 0.8479 (t0) cc_final: 0.8145 (t0) REVERT: M 55 GLU cc_start: 0.8655 (tt0) cc_final: 0.8371 (tt0) REVERT: M 59 ASN cc_start: 0.8925 (t0) cc_final: 0.8586 (m-40) REVERT: M 78 GLU cc_start: 0.7577 (tp30) cc_final: 0.7323 (mm-30) REVERT: N 121 GLN cc_start: 0.8415 (mp10) cc_final: 0.7784 (mp10) REVERT: P 21 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8526 (mp) REVERT: Q 44 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.7014 (p90) REVERT: V 49 ASN cc_start: 0.7574 (m110) cc_final: 0.7194 (m110) REVERT: V 121 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7637 (pp20) REVERT: V 128 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8519 (tp) REVERT: 1 4 TYR cc_start: 0.6977 (m-80) cc_final: 0.6693 (m-10) REVERT: 1 28 ASP cc_start: 0.7829 (t0) cc_final: 0.7510 (m-30) REVERT: 1 69 ASP cc_start: 0.7704 (m-30) cc_final: 0.7334 (m-30) outliers start: 111 outliers final: 56 residues processed: 480 average time/residue: 1.3029 time to fit residues: 774.6309 Evaluate side-chains 460 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 389 time to evaluate : 3.482 ------------------------------------------------------------------------------- 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 6 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 446 ASN 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 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 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 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 554 MET 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 283 LEU Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 375 VAL 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 22 VAL Chi-restraints excluded: chain M residue 75 SER 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 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 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 342 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 382 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 370 optimal weight: 0.3980 chunk 277 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 366 optimal weight: 0.7980 chunk 381 optimal weight: 0.9990 chunk 274 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 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 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN E 97 ASN G 97 GLN I 9 ASN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.081547 restraints weight = 70591.507| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.91 r_work: 0.3294 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33465 Z= 0.136 Angle : 0.752 46.893 45502 Z= 0.320 Chirality : 0.043 0.218 5209 Planarity : 0.005 0.070 5614 Dihedral : 9.480 107.477 5045 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.56 % Allowed : 20.59 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 4049 helix: 0.81 (0.11), residues: 2310 sheet: -2.65 (0.33), residues: 193 loop : -2.18 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 107 HIS 0.006 0.001 HIS D 247 PHE 0.031 0.001 PHE F 131 TYR 0.025 0.001 TYR L 31 ARG 0.011 0.000 ARG H 192 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 1658) hydrogen bonds : angle 4.16188 ( 4824) metal coordination : bond 0.01193 ( 16) metal coordination : angle 12.90566 ( 42) covalent geometry : bond 0.00314 (33449) covalent geometry : angle 0.64179 (45460) *********************** 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 527 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 407 time to evaluate : 3.468 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.6833 (p0) REVERT: A 90 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8677 (tm) REVERT: B 6 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5595 (pp) REVERT: D 250 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9171 (mp) REVERT: D 321 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8104 (tp) REVERT: D 413 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7811 (tm) REVERT: E 57 ILE cc_start: 0.8527 (mt) cc_final: 0.8224 (pt) REVERT: E 100 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8295 (mtpt) REVERT: F 193 MET cc_start: 0.8060 (ptm) cc_final: 0.7780 (ptm) REVERT: F 300 PHE cc_start: 0.8497 (t80) cc_final: 0.8205 (t80) REVERT: F 411 PHE cc_start: 0.8258 (m-10) cc_final: 0.8037 (m-10) REVERT: H 3 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6379 (pptt) REVERT: H 22 MET cc_start: 0.7014 (mtp) cc_final: 0.6047 (tmt) REVERT: H 340 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8881 (mp) REVERT: I 87 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: J 51 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7975 (tp-100) REVERT: J 100 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8733 (m) REVERT: K 27 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7529 (tp) REVERT: K 190 MET cc_start: 0.8626 (mtt) cc_final: 0.8299 (mtp) REVERT: L 47 MET cc_start: 0.8515 (mmt) cc_final: 0.8154 (mtp) REVERT: L 66 ASN cc_start: 0.8457 (t0) cc_final: 0.8144 (t0) REVERT: M 55 GLU cc_start: 0.8607 (tt0) cc_final: 0.8323 (tt0) REVERT: M 59 ASN cc_start: 0.8944 (t0) cc_final: 0.8621 (m-40) REVERT: M 78 GLU cc_start: 0.7530 (tp30) cc_final: 0.7261 (mm-30) REVERT: N 112 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7696 (mp0) REVERT: N 121 GLN cc_start: 0.8449 (mp10) cc_final: 0.7823 (mp10) REVERT: P 21 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8525 (mp) REVERT: Q 44 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.7008 (p90) REVERT: V 49 ASN cc_start: 0.7582 (m110) cc_final: 0.7235 (m110) REVERT: V 84 MET cc_start: 0.7856 (mmm) cc_final: 0.7191 (tmm) REVERT: V 121 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7666 (pp20) REVERT: V 128 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8572 (tp) REVERT: 1 4 TYR cc_start: 0.7040 (m-80) cc_final: 0.6726 (m-10) REVERT: 1 23 ASP cc_start: 0.6780 (m-30) cc_final: 0.6475 (m-30) REVERT: 1 28 ASP cc_start: 0.7850 (t0) cc_final: 0.7532 (m-30) REVERT: 1 55 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: 1 69 ASP cc_start: 0.7652 (m-30) cc_final: 0.7298 (m-30) outliers start: 120 outliers final: 57 residues processed: 493 average time/residue: 1.3773 time to fit residues: 833.8081 Evaluate side-chains 460 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 387 time to evaluate : 4.098 ------------------------------------------------------------------------------- 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 6 LEU Chi-restraints excluded: chain B residue 98 SER 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 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 21 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 250 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 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 513 VAL Chi-restraints excluded: chain F residue 554 MET 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 129 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 375 VAL 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 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 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 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 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 V residue 128 LEU Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 55 GLU 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 204 optimal weight: 0.9980 chunk 253 optimal weight: 6.9990 chunk 399 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 297 optimal weight: 0.0270 chunk 174 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN I 9 ASN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN S 64 GLN V 140 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.100371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.084350 restraints weight = 72710.535| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.02 r_work: 0.3282 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2472 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= 0.131 Angle : 0.782 47.472 45502 Z= 0.323 Chirality : 0.043 0.235 5209 Planarity : 0.005 0.069 5614 Dihedral : 9.334 107.681 5045 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.97 % Allowed : 21.45 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 4049 helix: 0.89 (0.11), residues: 2310 sheet: -2.65 (0.33), residues: 204 loop : -2.16 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 107 HIS 0.005 0.001 HIS D 247 PHE 0.036 0.001 PHE F 131 TYR 0.031 0.001 TYR H 182 ARG 0.012 0.000 ARG H 192 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 1658) hydrogen bonds : angle 4.15183 ( 4824) metal coordination : bond 0.01168 ( 16) metal coordination : angle 14.45107 ( 42) covalent geometry : bond 0.00299 (33449) covalent geometry : angle 0.64716 (45460) *********************** 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 510 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 410 time to evaluate : 3.652 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.6846 (p0) REVERT: A 90 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8658 (tm) REVERT: B 466 MET cc_start: 0.8336 (mmm) cc_final: 0.7872 (mtp) REVERT: D 321 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8144 (tp) REVERT: D 413 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7805 (tm) REVERT: D 498 ARG cc_start: 0.7257 (ttp80) cc_final: 0.6770 (ttp80) REVERT: E 57 ILE cc_start: 0.8492 (mt) cc_final: 0.8164 (pt) REVERT: E 93 MET cc_start: 0.8611 (mmm) cc_final: 0.8291 (mmp) REVERT: E 100 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8327 (mtpt) REVERT: F 193 MET cc_start: 0.8078 (ptm) cc_final: 0.7777 (ptm) REVERT: F 300 PHE cc_start: 0.8428 (t80) cc_final: 0.8103 (t80) REVERT: F 411 PHE cc_start: 0.8236 (m-10) cc_final: 0.8019 (m-10) REVERT: H 3 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6365 (pptt) REVERT: H 22 MET cc_start: 0.7003 (mtp) cc_final: 0.6027 (tmt) REVERT: H 373 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7452 (mtm) REVERT: I 87 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: J 51 GLN cc_start: 0.8243 (mm-40) cc_final: 0.8014 (tp-100) REVERT: J 100 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8729 (m) REVERT: K 27 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7510 (tp) REVERT: K 190 MET cc_start: 0.8675 (mtt) cc_final: 0.8380 (mtp) REVERT: L 47 MET cc_start: 0.8510 (mmt) cc_final: 0.7966 (mtp) REVERT: L 66 ASN cc_start: 0.8469 (t0) cc_final: 0.8174 (t0) REVERT: M 55 GLU cc_start: 0.8694 (tt0) cc_final: 0.8437 (tt0) REVERT: M 78 GLU cc_start: 0.7558 (tp30) cc_final: 0.7294 (mm-30) REVERT: N 112 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7738 (mp0) REVERT: N 121 GLN cc_start: 0.8426 (mp10) cc_final: 0.7716 (mp10) REVERT: Q 44 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.7017 (p90) REVERT: V 49 ASN cc_start: 0.7603 (m110) cc_final: 0.7317 (m-40) REVERT: V 84 MET cc_start: 0.7832 (mmm) cc_final: 0.7158 (tmm) REVERT: V 121 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7680 (pp20) REVERT: V 128 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8593 (tp) REVERT: V 140 GLN cc_start: 0.7685 (pt0) cc_final: 0.7378 (pt0) REVERT: 1 4 TYR cc_start: 0.7020 (m-80) cc_final: 0.6748 (m-10) REVERT: 1 8 LEU cc_start: 0.8747 (mm) cc_final: 0.8498 (mp) REVERT: 1 23 ASP cc_start: 0.6780 (m-30) cc_final: 0.6464 (m-30) REVERT: 1 28 ASP cc_start: 0.7858 (t0) cc_final: 0.7528 (m-30) REVERT: 1 55 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: 1 69 ASP cc_start: 0.7536 (m-30) cc_final: 0.7208 (m-30) outliers start: 100 outliers final: 56 residues processed: 478 average time/residue: 1.3970 time to fit residues: 830.4872 Evaluate side-chains 457 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 388 time to evaluate : 3.854 ------------------------------------------------------------------------------- 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 98 SER 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 21 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 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 434 LEU Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 554 MET 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 129 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 375 VAL 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 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 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL 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 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 93 SER Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 56 LEU 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 40 SER Chi-restraints excluded: chain 1 residue 55 GLU 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 360 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 378 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 389 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 336 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 118 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN I 9 ASN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.100551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.084574 restraints weight = 72564.986| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.00 r_work: 0.3303 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33465 Z= 0.131 Angle : 0.787 47.848 45502 Z= 0.326 Chirality : 0.043 0.257 5209 Planarity : 0.005 0.069 5614 Dihedral : 9.249 107.889 5045 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.70 % Allowed : 22.22 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 4049 helix: 0.91 (0.11), residues: 2315 sheet: -2.69 (0.34), residues: 187 loop : -2.14 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 107 HIS 0.021 0.001 HIS F 265 PHE 0.037 0.001 PHE F 131 TYR 0.027 0.001 TYR H 182 ARG 0.013 0.000 ARG H 192 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 1658) hydrogen bonds : angle 4.12788 ( 4824) metal coordination : bond 0.01158 ( 16) metal coordination : angle 14.42097 ( 42) covalent geometry : bond 0.00303 (33449) covalent geometry : angle 0.65377 (45460) *********************** 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: 91 poor density : 401 time to evaluate : 3.349 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.6871 (p0) REVERT: A 90 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8647 (tm) REVERT: B 466 MET cc_start: 0.8362 (mmm) cc_final: 0.7875 (mtp) REVERT: D 321 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8140 (tp) REVERT: D 413 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7800 (tm) REVERT: D 492 THR cc_start: 0.8496 (m) cc_final: 0.8201 (p) REVERT: E 100 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8310 (mtpt) REVERT: F 193 MET cc_start: 0.8077 (ptm) cc_final: 0.7774 (ptm) REVERT: F 300 PHE cc_start: 0.8498 (t80) cc_final: 0.8157 (t80) REVERT: F 411 PHE cc_start: 0.8222 (m-10) cc_final: 0.8000 (m-10) REVERT: H 3 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6377 (pptt) REVERT: H 22 MET cc_start: 0.6996 (mtp) cc_final: 0.6022 (tmt) REVERT: H 373 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7443 (mtm) REVERT: I 87 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7145 (pm20) REVERT: J 51 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8055 (tp-100) REVERT: J 100 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8749 (m) REVERT: K 27 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7454 (tp) REVERT: K 83 LEU cc_start: 0.9092 (tp) cc_final: 0.8788 (tp) REVERT: K 190 MET cc_start: 0.8654 (mtt) cc_final: 0.8360 (mtp) REVERT: L 47 MET cc_start: 0.8560 (mmt) cc_final: 0.8026 (mtp) REVERT: L 66 ASN cc_start: 0.8445 (t0) cc_final: 0.8162 (t0) REVERT: M 55 GLU cc_start: 0.8644 (tt0) cc_final: 0.8373 (tt0) REVERT: M 59 ASN cc_start: 0.8961 (t0) cc_final: 0.8632 (m-40) REVERT: M 78 GLU cc_start: 0.7535 (tp30) cc_final: 0.7274 (mm-30) REVERT: N 112 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7709 (mp0) REVERT: N 121 GLN cc_start: 0.8401 (mp10) cc_final: 0.7695 (mp10) REVERT: P 21 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8493 (mp) REVERT: Q 44 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.7068 (p90) REVERT: V 49 ASN cc_start: 0.7725 (m110) cc_final: 0.7415 (m-40) REVERT: V 84 MET cc_start: 0.7760 (mmm) cc_final: 0.7126 (tmm) REVERT: V 121 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7592 (pp20) REVERT: V 128 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8599 (tp) REVERT: V 140 GLN cc_start: 0.7700 (pt0) cc_final: 0.7365 (pt0) REVERT: 1 4 TYR cc_start: 0.7094 (m-80) cc_final: 0.6795 (m-10) REVERT: 1 8 LEU cc_start: 0.8686 (mm) cc_final: 0.8447 (mp) REVERT: 1 23 ASP cc_start: 0.6723 (m-30) cc_final: 0.6440 (m-30) REVERT: 1 28 ASP cc_start: 0.7863 (t0) cc_final: 0.7542 (m-30) REVERT: 1 55 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7549 (mp0) outliers start: 91 outliers final: 59 residues processed: 462 average time/residue: 1.2325 time to fit residues: 697.0805 Evaluate side-chains 458 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 385 time to evaluate : 3.815 ------------------------------------------------------------------------------- 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 98 SER 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 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 21 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 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 203 PHE 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 554 MET 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 129 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 375 VAL 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 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 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL 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 Q residue 9 ILE 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 121 GLU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 1 residue 55 GLU 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 178 optimal weight: 3.9990 chunk 325 optimal weight: 0.7980 chunk 266 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 359 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 317 optimal weight: 0.6980 chunk 335 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN I 9 ASN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.098756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.083351 restraints weight = 70442.409| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.91 r_work: 0.3302 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33465 Z= 0.143 Angle : 0.796 48.391 45502 Z= 0.331 Chirality : 0.044 0.282 5209 Planarity : 0.005 0.068 5614 Dihedral : 9.220 107.978 5045 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.34 % Allowed : 22.81 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 4049 helix: 0.94 (0.11), residues: 2307 sheet: -2.58 (0.35), residues: 187 loop : -2.12 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 107 HIS 0.016 0.001 HIS F 265 PHE 0.047 0.001 PHE V 44 TYR 0.027 0.001 TYR H 182 ARG 0.013 0.000 ARG H 192 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 1658) hydrogen bonds : angle 4.12419 ( 4824) metal coordination : bond 0.01279 ( 16) metal coordination : angle 14.48455 ( 42) covalent geometry : bond 0.00333 (33449) covalent geometry : angle 0.66409 (45460) ********************** 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 474 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 395 time to evaluate : 3.473 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.6834 (p0) REVERT: A 90 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8691 (tm) REVERT: B 466 MET cc_start: 0.8351 (mmm) cc_final: 0.7870 (mtp) REVERT: D 413 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7810 (tm) REVERT: D 492 THR cc_start: 0.8491 (m) cc_final: 0.8202 (p) REVERT: E 100 LYS cc_start: 0.8494 (mtmm) cc_final: 0.8225 (mtpt) REVERT: F 193 MET cc_start: 0.8075 (ptm) cc_final: 0.7763 (ptm) REVERT: F 300 PHE cc_start: 0.8451 (t80) cc_final: 0.8127 (t80) REVERT: F 411 PHE cc_start: 0.8226 (m-10) cc_final: 0.8006 (m-10) REVERT: H 22 MET cc_start: 0.6986 (mtp) cc_final: 0.6042 (tmt) REVERT: H 373 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7461 (mtm) REVERT: I 87 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7168 (pm20) REVERT: J 51 GLN cc_start: 0.8239 (mm-40) cc_final: 0.8015 (tp-100) REVERT: J 100 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8750 (m) REVERT: K 27 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7330 (tp) REVERT: K 83 LEU cc_start: 0.9080 (tp) cc_final: 0.8787 (tp) REVERT: K 190 MET cc_start: 0.8652 (mtt) cc_final: 0.8355 (mtp) REVERT: L 47 MET cc_start: 0.8551 (mmt) cc_final: 0.8134 (mtp) REVERT: L 66 ASN cc_start: 0.8460 (t0) cc_final: 0.8175 (t0) REVERT: M 55 GLU cc_start: 0.8597 (tt0) cc_final: 0.8298 (tt0) REVERT: M 59 ASN cc_start: 0.9005 (t0) cc_final: 0.8635 (m110) REVERT: M 78 GLU cc_start: 0.7502 (tp30) cc_final: 0.7232 (mm-30) REVERT: N 112 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7682 (mp0) REVERT: N 121 GLN cc_start: 0.8412 (mp10) cc_final: 0.7692 (mp10) REVERT: P 21 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8488 (mp) REVERT: Q 44 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.7023 (p90) REVERT: V 49 ASN cc_start: 0.7635 (m110) cc_final: 0.7328 (m-40) REVERT: V 84 MET cc_start: 0.7709 (mmm) cc_final: 0.7110 (tmm) REVERT: V 121 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7597 (pp20) REVERT: V 128 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8590 (tp) REVERT: V 140 GLN cc_start: 0.7722 (pt0) cc_final: 0.7392 (pt0) REVERT: 1 1 MET cc_start: 0.5746 (mpt) cc_final: 0.4198 (tpp) REVERT: 1 4 TYR cc_start: 0.7113 (m-80) cc_final: 0.6817 (m-10) REVERT: 1 8 LEU cc_start: 0.8683 (mm) cc_final: 0.8325 (mp) REVERT: 1 23 ASP cc_start: 0.6685 (m-30) cc_final: 0.6193 (m-30) REVERT: 1 28 ASP cc_start: 0.7883 (t0) cc_final: 0.7564 (m-30) REVERT: 1 69 ASP cc_start: 0.7489 (m-30) cc_final: 0.7223 (m-30) outliers start: 79 outliers final: 59 residues processed: 452 average time/residue: 1.2199 time to fit residues: 674.7312 Evaluate side-chains 455 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 385 time to evaluate : 3.333 ------------------------------------------------------------------------------- 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 98 SER 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 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 21 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 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 203 PHE 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 554 MET 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 375 VAL 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 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 135 VAL Chi-restraints excluded: chain L residue 13 TYR Chi-restraints excluded: chain L residue 38 VAL 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 Q residue 9 ILE 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 121 GLU Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 128 LEU 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 46 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 379 optimal weight: 0.9980 chunk 230 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 322 optimal weight: 0.0570 chunk 289 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 375 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.098608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.083177 restraints weight = 70210.241| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.90 r_work: 0.3298 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33465 Z= 0.145 Angle : 0.796 48.620 45502 Z= 0.331 Chirality : 0.044 0.277 5209 Planarity : 0.005 0.072 5614 Dihedral : 9.183 107.000 5045 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.37 % Allowed : 22.96 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 4049 helix: 0.97 (0.11), residues: 2304 sheet: -2.64 (0.36), residues: 183 loop : -2.07 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 107 HIS 0.016 0.001 HIS F 265 PHE 0.045 0.001 PHE V 44 TYR 0.026 0.001 TYR H 182 ARG 0.013 0.000 ARG H 192 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 1658) hydrogen bonds : angle 4.13044 ( 4824) metal coordination : bond 0.01322 ( 16) metal coordination : angle 14.52229 ( 42) covalent geometry : bond 0.00339 (33449) covalent geometry : angle 0.66340 (45460) =============================================================================== Job complete usr+sys time: 27634.48 seconds wall clock time: 478 minutes 40.74 seconds (28720.74 seconds total)