Starting phenix.real_space_refine on Wed Apr 30 14:11:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pr4_17834/04_2025/8pr4_17834.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pr4_17834/04_2025/8pr4_17834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pr4_17834/04_2025/8pr4_17834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pr4_17834/04_2025/8pr4_17834.map" model { file = "/net/cci-nas-00/data/ceres_data/8pr4_17834/04_2025/8pr4_17834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pr4_17834/04_2025/8pr4_17834.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 3 5.49 5 S 57 5.16 5 C 6006 2.51 5 N 1680 2.21 5 O 1745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9494 Number of models: 1 Model: "" Number of chains: 8 Chain: "J" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2932 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 354} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "U" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1262 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "W" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1314 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 168} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "Y" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2793 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 26, 'TRANS': 348} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 11, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "X" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 704 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 200 Chain: "x" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 455 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 190 Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5742 SG CYS Y 30 46.962 79.433 50.441 1.00119.87 S ATOM 5771 SG CYS Y 33 43.721 80.939 49.654 1.00124.84 S ATOM 7246 SG CYS Y 284 44.584 77.361 48.253 1.00116.63 S ATOM 7272 SG CYS Y 287 45.916 80.687 46.863 1.00123.33 S ATOM 5910 SG CYS Y 51 61.662 49.335 53.098 1.00110.92 S ATOM 5929 SG CYS Y 54 65.386 48.865 52.682 1.00119.02 S ATOM 6054 SG CYS Y 70 62.803 47.547 49.966 1.00105.43 S ATOM 6073 SG CYS Y 73 63.592 46.023 53.433 1.00101.62 S ATOM 6095 SG CYS Y 76 55.015 37.387 59.347 1.00 97.69 S ATOM 6112 SG CYS Y 79 54.120 38.479 62.481 1.00106.11 S ATOM 6229 SG CYS Y 111 57.893 37.578 61.880 1.00 98.28 S ATOM 6250 SG CYS Y 114 55.392 34.862 62.376 1.00 94.54 S Time building chain proxies: 7.25, per 1000 atoms: 0.76 Number of scatterers: 9494 At special positions: 0 Unit cell: (109.077, 106.959, 110.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 57 16.00 P 3 15.00 O 1745 8.00 N 1680 7.00 C 6006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y 501 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 287 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 30 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 284 " pdb=" ZN Y 502 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 73 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 54 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 51 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 70 " pdb=" ZN Y 503 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 76 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 79 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 111 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 114 " Number of angles added : 18 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2482 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 24 sheets defined 33.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'J' and resid 60 through 79 removed outlier: 3.635A pdb=" N LEU J 64 " --> pdb=" O ASN J 60 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS J 79 " --> pdb=" O LEU J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 112 Processing helix chain 'J' and resid 124 through 129 Processing helix chain 'J' and resid 158 through 161 removed outlier: 3.973A pdb=" N TRP J 161 " --> pdb=" O LEU J 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 158 through 161' Processing helix chain 'J' and resid 167 through 182 removed outlier: 3.593A pdb=" N LEU J 171 " --> pdb=" O GLY J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 214 Processing helix chain 'J' and resid 219 through 232 removed outlier: 3.598A pdb=" N LYS J 225 " --> pdb=" O THR J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 266 Processing helix chain 'J' and resid 267 through 270 Processing helix chain 'J' and resid 281 through 289 removed outlier: 3.923A pdb=" N LEU J 285 " --> pdb=" O ALA J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 301 Processing helix chain 'J' and resid 314 through 327 Processing helix chain 'J' and resid 329 through 337 removed outlier: 4.395A pdb=" N LYS J 334 " --> pdb=" O PRO J 330 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR J 335 " --> pdb=" O LYS J 331 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY J 337 " --> pdb=" O LYS J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 363 removed outlier: 3.655A pdb=" N ALA J 363 " --> pdb=" O ALA J 359 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 369 removed outlier: 4.449A pdb=" N GLY J 369 " --> pdb=" O GLN J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 375 through 381 Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.881A pdb=" N ASN U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE U 70 " --> pdb=" O HIS U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'U' and resid 161 through 168 Processing helix chain 'W' and resid 164 through 175 Processing helix chain 'Y' and resid 23 through 25 No H-bonds generated for 'chain 'Y' and resid 23 through 25' Processing helix chain 'Y' and resid 59 through 66 Processing helix chain 'Y' and resid 138 through 140 No H-bonds generated for 'chain 'Y' and resid 138 through 140' Processing helix chain 'Y' and resid 141 through 170 removed outlier: 3.858A pdb=" N GLN Y 153 " --> pdb=" O GLU Y 149 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU Y 161 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG Y 162 " --> pdb=" O GLU Y 158 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP Y 163 " --> pdb=" O LYS Y 159 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG Y 164 " --> pdb=" O VAL Y 160 " (cutoff:3.500A) Processing helix chain 'Y' and resid 251 through 256 Processing helix chain 'Y' and resid 265 through 269 removed outlier: 3.765A pdb=" N GLN Y 268 " --> pdb=" O CYS Y 265 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU Y 269 " --> pdb=" O ALA Y 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 265 through 269' Processing helix chain 'Y' and resid 308 through 312 Processing helix chain 'Y' and resid 448 through 452 removed outlier: 3.572A pdb=" N VAL Y 451 " --> pdb=" O GLY Y 448 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER Y 452 " --> pdb=" O ALA Y 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 448 through 452' Processing helix chain 'X' and resid 382 through 387 Processing helix chain 'X' and resid 391 through 396 Processing helix chain 'X' and resid 412 through 467 removed outlier: 3.807A pdb=" N VAL X 420 " --> pdb=" O MET X 416 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU X 423 " --> pdb=" O GLU X 419 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU X 425 " --> pdb=" O GLY X 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU X 430 " --> pdb=" O GLU X 426 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL X 439 " --> pdb=" O ASN X 435 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL X 440 " --> pdb=" O ALA X 436 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA X 446 " --> pdb=" O ASN X 442 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS X 447 " --> pdb=" O ASP X 443 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP X 449 " --> pdb=" O ILE X 445 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN X 450 " --> pdb=" O ALA X 446 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU X 451 " --> pdb=" O LYS X 447 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL X 457 " --> pdb=" O GLY X 453 " (cutoff:3.500A) Processing helix chain 'X' and resid 519 through 549 Processing helix chain 'x' and resid 411 through 467 removed outlier: 3.839A pdb=" N VAL x 440 " --> pdb=" O ALA x 436 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU x 462 " --> pdb=" O LEU x 458 " (cutoff:3.500A) Processing helix chain 'x' and resid 519 through 540 removed outlier: 3.588A pdb=" N TYR x 538 " --> pdb=" O GLU x 534 " (cutoff:3.500A) Processing helix chain 'x' and resid 540 through 551 removed outlier: 3.949A pdb=" N GLU x 544 " --> pdb=" O GLU x 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 37 through 40 removed outlier: 6.443A pdb=" N VAL J 16 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE J 92 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE J 18 " --> pdb=" O ILE J 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL J 118 " --> pdb=" O VAL J 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'J' and resid 135 through 141 Processing sheet with id=AA4, first strand: chain 'J' and resid 135 through 141 removed outlier: 3.600A pdb=" N LEU J 164 " --> pdb=" O SER J 146 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY J 162 " --> pdb=" O VAL J 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 185 through 186 Processing sheet with id=AA6, first strand: chain 'U' and resid 9 through 11 removed outlier: 6.199A pdb=" N THR U 28 " --> pdb=" O ILE U 50 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL U 49 " --> pdb=" O ILE U 84 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE U 83 " --> pdb=" O MET U 101 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS U 100 " --> pdb=" O LEU U 119 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE U 118 " --> pdb=" O ILE U 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'U' and resid 16 through 17 removed outlier: 7.183A pdb=" N VAL U 16 " --> pdb=" O ILE U 35 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL U 34 " --> pdb=" O ILE U 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'U' and resid 23 through 24 removed outlier: 6.004A pdb=" N LEU U 61 " --> pdb=" O SER U 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 106 through 107 removed outlier: 6.755A pdb=" N VAL U 106 " --> pdb=" O ILE U 125 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE U 124 " --> pdb=" O ILE U 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'U' and resid 112 through 113 removed outlier: 6.146A pdb=" N TYR U 112 " --> pdb=" O LEU U 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'W' and resid 6 through 8 removed outlier: 3.510A pdb=" N LEU W 177 " --> pdb=" O LEU W 6 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR W 8 " --> pdb=" O LEU W 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'W' and resid 13 through 15 removed outlier: 6.476A pdb=" N LYS W 21 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE W 41 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL W 62 " --> pdb=" O ILE W 93 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE W 92 " --> pdb=" O VAL W 110 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS W 109 " --> pdb=" O ILE W 128 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL W 145 " --> pdb=" O SER W 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 28 through 29 Processing sheet with id=AB5, first strand: chain 'W' and resid 35 through 36 removed outlier: 7.099A pdb=" N VAL W 35 " --> pdb=" O VAL W 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'W' and resid 68 through 69 removed outlier: 6.683A pdb=" N VAL W 68 " --> pdb=" O VAL W 99 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL W 98 " --> pdb=" O ILE W 116 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL W 115 " --> pdb=" O LEU W 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'W' and resid 73 through 74 removed outlier: 3.907A pdb=" N LYS W 74 " --> pdb=" O ALA W 81 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA W 81 " --> pdb=" O LYS W 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'W' and resid 121 through 122 removed outlier: 7.259A pdb=" N VAL W 121 " --> pdb=" O VAL W 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'Y' and resid 21 through 22 removed outlier: 5.028A pdb=" N HIS Y 457 " --> pdb=" O LEU Y 13 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 27 through 30 removed outlier: 3.934A pdb=" N GLU Y 35 " --> pdb=" O CYS Y 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 43 through 44 removed outlier: 6.565A pdb=" N LEU Y 282 " --> pdb=" O LEU Y 291 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Y' and resid 57 through 58 removed outlier: 4.084A pdb=" N HIS Y 49 " --> pdb=" O MET Y 58 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER Y 48 " --> pdb=" O LYS Y 279 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 69 through 75 removed outlier: 4.510A pdb=" N LYS Y 274 " --> pdb=" O CYS Y 70 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ASN Y 72 " --> pdb=" O ARG Y 272 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ARG Y 272 " --> pdb=" O ASN Y 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 84 through 86 Processing sheet with id=AC6, first strand: chain 'Y' and resid 316 through 320 removed outlier: 3.822A pdb=" N MET Y 319 " --> pdb=" O GLN Y 331 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLN Y 331 " --> pdb=" O MET Y 319 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS Y 406 " --> pdb=" O LYS Y 403 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE Y 401 " --> pdb=" O GLY Y 408 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE Y 410 " --> pdb=" O VAL Y 399 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL Y 399 " --> pdb=" O PHE Y 410 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1059 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: 2.94 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 1 1.20 - 1.36: 3205 1.36 - 1.51: 2860 1.51 - 1.67: 3515 1.67 - 1.83: 75 Bond restraints: 9656 Sorted by residual: bond pdb=" CG PRO Y 369 " pdb=" CD PRO Y 369 " ideal model delta sigma weight residual 1.503 1.043 0.460 3.40e-02 8.65e+02 1.83e+02 bond pdb=" N PRO Y 369 " pdb=" CD PRO Y 369 " ideal model delta sigma weight residual 1.473 1.572 -0.099 1.40e-02 5.10e+03 4.95e+01 bond pdb=" C PHE Y 392 " pdb=" N PRO Y 393 " ideal model delta sigma weight residual 1.334 1.407 -0.073 2.34e-02 1.83e+03 9.82e+00 bond pdb=" C ALA U 146 " pdb=" O ALA U 146 " ideal model delta sigma weight residual 1.236 1.270 -0.033 1.26e-02 6.30e+03 7.03e+00 bond pdb=" CB ASN J 275 " pdb=" CG ASN J 275 " ideal model delta sigma weight residual 1.516 1.580 -0.064 2.50e-02 1.60e+03 6.59e+00 ... (remaining 9651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.47: 13049 5.47 - 10.95: 84 10.95 - 16.42: 13 16.42 - 21.90: 6 21.90 - 27.37: 2 Bond angle restraints: 13154 Sorted by residual: angle pdb=" N PRO Y 369 " pdb=" CD PRO Y 369 " pdb=" CG PRO Y 369 " ideal model delta sigma weight residual 103.20 78.30 24.90 1.50e+00 4.44e-01 2.76e+02 angle pdb=" CA PRO Y 369 " pdb=" N PRO Y 369 " pdb=" CD PRO Y 369 " ideal model delta sigma weight residual 112.00 95.75 16.25 1.40e+00 5.10e-01 1.35e+02 angle pdb=" CA PRO Y 369 " pdb=" CB PRO Y 369 " pdb=" CG PRO Y 369 " ideal model delta sigma weight residual 104.50 85.53 18.97 1.90e+00 2.77e-01 9.97e+01 angle pdb=" CA LEU J 96 " pdb=" CB LEU J 96 " pdb=" CG LEU J 96 " ideal model delta sigma weight residual 116.30 143.67 -27.37 3.50e+00 8.16e-02 6.12e+01 angle pdb=" CB MET Y 144 " pdb=" CG MET Y 144 " pdb=" SD MET Y 144 " ideal model delta sigma weight residual 112.70 130.37 -17.67 3.00e+00 1.11e-01 3.47e+01 ... (remaining 13149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 5005 16.62 - 33.24: 615 33.24 - 49.85: 208 49.85 - 66.47: 34 66.47 - 83.09: 13 Dihedral angle restraints: 5875 sinusoidal: 2049 harmonic: 3826 Sorted by residual: dihedral pdb=" CA MET J 126 " pdb=" C MET J 126 " pdb=" N ALA J 127 " pdb=" CA ALA J 127 " ideal model delta harmonic sigma weight residual 180.00 146.03 33.97 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA MET J 311 " pdb=" C MET J 311 " pdb=" N LEU J 312 " pdb=" CA LEU J 312 " ideal model delta harmonic sigma weight residual 180.00 154.92 25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLN J 298 " pdb=" C GLN J 298 " pdb=" N LEU J 299 " pdb=" CA LEU J 299 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 5872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1387 0.106 - 0.211: 168 0.211 - 0.317: 14 0.317 - 0.423: 2 0.423 - 0.528: 1 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CB VAL J 82 " pdb=" CA VAL J 82 " pdb=" CG1 VAL J 82 " pdb=" CG2 VAL J 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.53 2.00e-01 2.50e+01 6.98e+00 chirality pdb=" CG LEU Y 282 " pdb=" CB LEU Y 282 " pdb=" CD1 LEU Y 282 " pdb=" CD2 LEU Y 282 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA ASN J 275 " pdb=" N ASN J 275 " pdb=" C ASN J 275 " pdb=" CB ASN J 275 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 1569 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO Y 368 " -0.118 5.00e-02 4.00e+02 1.62e-01 4.20e+01 pdb=" N PRO Y 369 " 0.279 5.00e-02 4.00e+02 pdb=" CA PRO Y 369 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO Y 369 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 387 " -0.020 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" CG TRP J 387 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP J 387 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP J 387 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP J 387 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 387 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J 387 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 387 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 387 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 387 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU W 15 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" CD GLU W 15 " -0.066 2.00e-02 2.50e+03 pdb=" OE1 GLU W 15 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU W 15 " 0.023 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2836 2.83 - 3.35: 7760 3.35 - 3.86: 16170 3.86 - 4.38: 16620 4.38 - 4.90: 29344 Nonbonded interactions: 72730 Sorted by model distance: nonbonded pdb=" O ARG X 541 " pdb=" N GLU X 544 " model vdw 2.309 3.120 nonbonded pdb=" OG1 THR U 33 " pdb=" O ASN U 54 " model vdw 2.323 3.040 nonbonded pdb=" O TYR J 377 " pdb=" OG1 THR J 381 " model vdw 2.347 3.040 nonbonded pdb=" OG SER W 18 " pdb=" OD1 ASN W 20 " model vdw 2.350 3.040 nonbonded pdb=" O THR X 379 " pdb=" OG1 THR X 379 " model vdw 2.370 3.040 ... (remaining 72725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.540 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.910 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 0.460 9668 Z= 0.370 Angle : 1.352 27.371 13172 Z= 0.710 Chirality : 0.068 0.528 1572 Planarity : 0.011 0.162 1702 Dihedral : 17.206 83.088 3393 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.48 % Favored : 92.36 % Rotamer: Outliers : 1.00 % Allowed : 28.76 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.40 (0.19), residues: 1296 helix: -2.79 (0.18), residues: 402 sheet: -1.59 (0.36), residues: 190 loop : -2.10 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.005 TRP J 387 HIS 0.007 0.001 HIS W 90 PHE 0.029 0.002 PHE W 83 TYR 0.018 0.002 TYR J 76 ARG 0.023 0.001 ARG U 156 Details of bonding type rmsd hydrogen bonds : bond 0.13780 ( 366) hydrogen bonds : angle 7.19128 ( 1059) metal coordination : bond 0.00822 ( 12) metal coordination : angle 6.50174 ( 18) covalent geometry : bond 0.00833 ( 9656) covalent geometry : angle 1.33090 (13154) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7629 (t80) outliers start: 9 outliers final: 2 residues processed: 94 average time/residue: 0.1923 time to fit residues: 27.0697 Evaluate side-chains 80 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain U residue 131 LEU Chi-restraints excluded: chain Y residue 305 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.0020 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 HIS J 351 ASN ** J 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 138 HIS Y 253 GLN X 378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.074688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.056507 restraints weight = 31562.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.058402 restraints weight = 16537.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.059669 restraints weight = 11091.375| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9668 Z= 0.209 Angle : 0.664 12.738 13172 Z= 0.328 Chirality : 0.045 0.143 1572 Planarity : 0.006 0.068 1702 Dihedral : 6.563 68.556 1435 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.12 % Allowed : 25.31 % Favored : 70.57 % 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: -1.65 (0.22), residues: 1296 helix: 0.12 (0.25), residues: 404 sheet: -1.46 (0.36), residues: 211 loop : -1.74 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 387 HIS 0.003 0.001 HIS Y 430 PHE 0.010 0.001 PHE Y 74 TYR 0.009 0.001 TYR Y 312 ARG 0.004 0.000 ARG W 49 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 366) hydrogen bonds : angle 4.43947 ( 1059) metal coordination : bond 0.00976 ( 12) metal coordination : angle 4.09219 ( 18) covalent geometry : bond 0.00480 ( 9656) covalent geometry : angle 0.64694 (13154) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7647 (t80) REVERT: J 365 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7357 (mt0) REVERT: U 123 CYS cc_start: 0.8685 (p) cc_final: 0.8414 (m) REVERT: U 125 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8803 (mp) REVERT: Y 253 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8570 (tp-100) REVERT: Y 261 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8335 (p90) REVERT: Y 319 MET cc_start: 0.8446 (pmm) cc_final: 0.8028 (pmm) outliers start: 37 outliers final: 16 residues processed: 105 average time/residue: 0.1768 time to fit residues: 28.1202 Evaluate side-chains 87 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 351 ASN Chi-restraints excluded: chain J residue 352 CYS Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 148 CYS Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain Y residue 221 ILE Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 253 GLN Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 297 ASN Chi-restraints excluded: chain Y residue 305 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 81 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 380 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.074842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.056721 restraints weight = 31721.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058621 restraints weight = 16506.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059924 restraints weight = 11022.811| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9668 Z= 0.155 Angle : 0.599 11.565 13172 Z= 0.292 Chirality : 0.044 0.143 1572 Planarity : 0.005 0.042 1702 Dihedral : 5.898 74.072 1433 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.57 % Allowed : 24.53 % Favored : 70.90 % 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: -0.85 (0.24), residues: 1296 helix: 1.34 (0.27), residues: 410 sheet: -1.46 (0.36), residues: 212 loop : -1.51 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 387 HIS 0.002 0.001 HIS W 109 PHE 0.008 0.001 PHE U 134 TYR 0.008 0.001 TYR Y 32 ARG 0.002 0.000 ARG U 156 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 366) hydrogen bonds : angle 4.09059 ( 1059) metal coordination : bond 0.00785 ( 12) metal coordination : angle 3.45003 ( 18) covalent geometry : bond 0.00356 ( 9656) covalent geometry : angle 0.58608 (13154) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 69 time to evaluate : 1.328 Fit side-chains REVERT: J 76 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7750 (t80) REVERT: J 365 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7327 (mt0) REVERT: J 380 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8038 (pp30) REVERT: U 125 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8799 (mp) REVERT: W 37 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7176 (p0) REVERT: W 176 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8868 (t80) REVERT: Y 261 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8262 (p90) REVERT: Y 319 MET cc_start: 0.8235 (pmm) cc_final: 0.7981 (pmm) REVERT: X 380 ASP cc_start: 0.7948 (t0) cc_final: 0.7725 (t0) outliers start: 41 outliers final: 21 residues processed: 105 average time/residue: 0.2300 time to fit residues: 37.0813 Evaluate side-chains 92 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain J residue 380 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 37 ASN Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 221 ILE Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 297 ASN Chi-restraints excluded: chain Y residue 305 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 22 optimal weight: 0.0370 chunk 6 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 275 ASN W 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.075564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.057478 restraints weight = 31439.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059407 restraints weight = 16315.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.060668 restraints weight = 10893.936| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9668 Z= 0.110 Angle : 0.560 10.717 13172 Z= 0.270 Chirality : 0.043 0.145 1572 Planarity : 0.004 0.038 1702 Dihedral : 5.503 75.461 1433 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.57 % Allowed : 25.75 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1296 helix: 1.98 (0.27), residues: 411 sheet: -1.40 (0.36), residues: 212 loop : -1.30 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 387 HIS 0.002 0.000 HIS W 109 PHE 0.008 0.001 PHE J 113 TYR 0.009 0.001 TYR Y 32 ARG 0.002 0.000 ARG U 156 Details of bonding type rmsd hydrogen bonds : bond 0.03032 ( 366) hydrogen bonds : angle 3.83615 ( 1059) metal coordination : bond 0.00568 ( 12) metal coordination : angle 3.10404 ( 18) covalent geometry : bond 0.00259 ( 9656) covalent geometry : angle 0.54837 (13154) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7817 (t80) REVERT: J 365 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7307 (mt0) REVERT: W 37 ASN cc_start: 0.7319 (OUTLIER) cc_final: 0.7008 (p0) REVERT: W 162 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7907 (tp40) REVERT: Y 261 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8246 (p90) outliers start: 32 outliers final: 16 residues processed: 98 average time/residue: 0.2102 time to fit residues: 31.8078 Evaluate side-chains 85 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 275 ASN Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 37 ASN Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 297 ASN Chi-restraints excluded: chain Y residue 305 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.071521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.053760 restraints weight = 32692.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.055528 restraints weight = 17383.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.056723 restraints weight = 11813.060| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9668 Z= 0.242 Angle : 0.639 9.799 13172 Z= 0.312 Chirality : 0.045 0.172 1572 Planarity : 0.004 0.037 1702 Dihedral : 5.697 71.010 1433 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.13 % Allowed : 23.97 % Favored : 70.90 % 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: -0.24 (0.24), residues: 1296 helix: 2.15 (0.27), residues: 416 sheet: -1.53 (0.36), residues: 195 loop : -1.24 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 387 HIS 0.003 0.001 HIS U 36 PHE 0.010 0.001 PHE Y 74 TYR 0.007 0.001 TYR J 378 ARG 0.002 0.000 ARG U 156 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 366) hydrogen bonds : angle 3.88916 ( 1059) metal coordination : bond 0.01046 ( 12) metal coordination : angle 3.50856 ( 18) covalent geometry : bond 0.00554 ( 9656) covalent geometry : angle 0.62610 (13154) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 64 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.7841 (t80) REVERT: J 126 MET cc_start: 0.9001 (mtm) cc_final: 0.8364 (mtm) REVERT: J 137 MET cc_start: 0.7765 (tpp) cc_final: 0.7549 (tpp) REVERT: J 365 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7314 (mt0) REVERT: J 380 GLN cc_start: 0.8450 (pp30) cc_final: 0.8138 (pp30) REVERT: U 125 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8759 (mp) REVERT: W 37 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.7258 (p0) REVERT: W 176 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8857 (t80) REVERT: Y 261 PHE cc_start: 0.9296 (OUTLIER) cc_final: 0.8289 (p90) outliers start: 46 outliers final: 27 residues processed: 107 average time/residue: 0.1802 time to fit residues: 29.3890 Evaluate side-chains 96 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 63 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 37 ASN Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 239 TYR Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 297 ASN Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain X residue 393 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 89 optimal weight: 0.1980 chunk 48 optimal weight: 0.0470 chunk 124 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.073239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.055585 restraints weight = 31996.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.057387 restraints weight = 17150.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.058596 restraints weight = 11627.868| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9668 Z= 0.113 Angle : 0.563 10.042 13172 Z= 0.272 Chirality : 0.043 0.147 1572 Planarity : 0.004 0.036 1702 Dihedral : 5.345 75.517 1433 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.68 % Allowed : 25.64 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.25), residues: 1296 helix: 2.46 (0.27), residues: 416 sheet: -1.53 (0.36), residues: 206 loop : -1.12 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 355 HIS 0.001 0.000 HIS J 79 PHE 0.007 0.001 PHE U 134 TYR 0.008 0.001 TYR Y 32 ARG 0.003 0.000 ARG U 156 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 366) hydrogen bonds : angle 3.66854 ( 1059) metal coordination : bond 0.00594 ( 12) metal coordination : angle 3.09851 ( 18) covalent geometry : bond 0.00265 ( 9656) covalent geometry : angle 0.55199 (13154) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.7943 (t80) REVERT: J 137 MET cc_start: 0.7656 (tpp) cc_final: 0.7436 (tpp) REVERT: J 365 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7279 (mt0) REVERT: J 380 GLN cc_start: 0.8391 (pp30) cc_final: 0.8019 (pp30) REVERT: U 125 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8683 (mp) REVERT: W 37 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7090 (p0) REVERT: W 176 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8828 (t80) REVERT: Y 261 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8232 (p90) outliers start: 33 outliers final: 20 residues processed: 102 average time/residue: 0.1952 time to fit residues: 29.4395 Evaluate side-chains 90 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 37 ASN Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 305 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 80 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 22 optimal weight: 0.3980 chunk 122 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.072679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.055072 restraints weight = 32289.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.056863 restraints weight = 17034.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.058081 restraints weight = 11513.511| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9668 Z= 0.148 Angle : 0.573 9.826 13172 Z= 0.279 Chirality : 0.044 0.146 1572 Planarity : 0.004 0.036 1702 Dihedral : 5.288 73.040 1433 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.68 % Allowed : 24.64 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.25), residues: 1296 helix: 2.61 (0.27), residues: 416 sheet: -1.47 (0.35), residues: 218 loop : -1.10 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 355 HIS 0.002 0.001 HIS J 79 PHE 0.007 0.001 PHE Y 296 TYR 0.007 0.001 TYR Y 32 ARG 0.001 0.000 ARG J 102 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 366) hydrogen bonds : angle 3.62610 ( 1059) metal coordination : bond 0.00728 ( 12) metal coordination : angle 3.12667 ( 18) covalent geometry : bond 0.00343 ( 9656) covalent geometry : angle 0.56154 (13154) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 66 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.7995 (t80) REVERT: J 137 MET cc_start: 0.7618 (tpp) cc_final: 0.7386 (tpp) REVERT: J 365 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7334 (mt0) REVERT: U 125 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8677 (mp) REVERT: W 37 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.7135 (p0) REVERT: W 176 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8823 (t80) REVERT: Y 261 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8202 (p90) outliers start: 42 outliers final: 27 residues processed: 104 average time/residue: 0.1964 time to fit residues: 30.2281 Evaluate side-chains 97 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 37 ASN Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 118 ARG Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 221 ILE Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 239 TYR Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 305 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.072988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.055219 restraints weight = 32599.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.057027 restraints weight = 17449.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058242 restraints weight = 11858.503| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9668 Z= 0.135 Angle : 0.575 10.669 13172 Z= 0.278 Chirality : 0.043 0.147 1572 Planarity : 0.003 0.035 1702 Dihedral : 5.160 73.645 1433 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.12 % Allowed : 25.31 % Favored : 70.57 % 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: 0.18 (0.25), residues: 1296 helix: 2.73 (0.27), residues: 417 sheet: -1.46 (0.35), residues: 220 loop : -1.06 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 355 HIS 0.001 0.001 HIS J 79 PHE 0.007 0.001 PHE U 134 TYR 0.008 0.001 TYR Y 32 ARG 0.002 0.000 ARG Y 143 Details of bonding type rmsd hydrogen bonds : bond 0.02898 ( 366) hydrogen bonds : angle 3.54779 ( 1059) metal coordination : bond 0.00672 ( 12) metal coordination : angle 3.13750 ( 18) covalent geometry : bond 0.00317 ( 9656) covalent geometry : angle 0.56403 (13154) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.7990 (t80) REVERT: J 126 MET cc_start: 0.8750 (mtm) cc_final: 0.8444 (mtm) REVERT: J 137 MET cc_start: 0.7515 (tpp) cc_final: 0.7267 (tpp) REVERT: J 365 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: J 380 GLN cc_start: 0.8495 (pp30) cc_final: 0.7958 (pp30) REVERT: U 125 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8672 (mp) REVERT: W 37 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.7050 (p0) REVERT: W 176 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8779 (t80) REVERT: Y 261 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8218 (p90) outliers start: 37 outliers final: 24 residues processed: 101 average time/residue: 0.1909 time to fit residues: 28.4849 Evaluate side-chains 96 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain W residue 37 ASN Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 239 TYR Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain X residue 393 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 88 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 68 optimal weight: 0.0050 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.0030 chunk 99 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 379 ASN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.073982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.056370 restraints weight = 31853.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.058181 restraints weight = 16727.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.059466 restraints weight = 11317.232| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9668 Z= 0.103 Angle : 0.549 9.527 13172 Z= 0.265 Chirality : 0.043 0.146 1572 Planarity : 0.003 0.034 1702 Dihedral : 4.923 72.792 1433 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.12 % Allowed : 25.98 % Favored : 70.90 % 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: 0.41 (0.25), residues: 1296 helix: 2.96 (0.27), residues: 411 sheet: -1.32 (0.35), residues: 224 loop : -0.92 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 355 HIS 0.002 0.000 HIS Y 49 PHE 0.007 0.001 PHE U 134 TYR 0.008 0.001 TYR Y 32 ARG 0.003 0.000 ARG U 156 Details of bonding type rmsd hydrogen bonds : bond 0.02723 ( 366) hydrogen bonds : angle 3.42080 ( 1059) metal coordination : bond 0.00508 ( 12) metal coordination : angle 3.01511 ( 18) covalent geometry : bond 0.00243 ( 9656) covalent geometry : angle 0.53769 (13154) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.7907 (t80) REVERT: J 365 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: J 380 GLN cc_start: 0.8427 (pp30) cc_final: 0.7943 (pp30) REVERT: U 125 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8666 (mp) REVERT: W 37 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.6965 (p0) REVERT: W 176 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8790 (t80) REVERT: Y 261 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8360 (p90) outliers start: 28 outliers final: 21 residues processed: 97 average time/residue: 0.1828 time to fit residues: 26.2374 Evaluate side-chains 95 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain W residue 37 ASN Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 118 ARG Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain X residue 393 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 20.0000 chunk 68 optimal weight: 0.3980 chunk 90 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 127 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.056101 restraints weight = 32208.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.057952 restraints weight = 16853.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.059206 restraints weight = 11317.387| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9668 Z= 0.114 Angle : 0.582 10.615 13172 Z= 0.277 Chirality : 0.043 0.146 1572 Planarity : 0.003 0.034 1702 Dihedral : 4.916 71.695 1433 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.12 % Allowed : 26.42 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.46 (0.25), residues: 1296 helix: 2.98 (0.26), residues: 411 sheet: -1.31 (0.35), residues: 225 loop : -0.86 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 355 HIS 0.001 0.000 HIS J 79 PHE 0.007 0.001 PHE W 83 TYR 0.007 0.001 TYR Y 32 ARG 0.003 0.000 ARG U 156 Details of bonding type rmsd hydrogen bonds : bond 0.02728 ( 366) hydrogen bonds : angle 3.40338 ( 1059) metal coordination : bond 0.00585 ( 12) metal coordination : angle 2.99913 ( 18) covalent geometry : bond 0.00271 ( 9656) covalent geometry : angle 0.57149 (13154) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.7915 (t80) REVERT: J 365 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7390 (mt0) REVERT: J 380 GLN cc_start: 0.8446 (pp30) cc_final: 0.7945 (pp30) REVERT: U 125 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8629 (mp) REVERT: W 37 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.7021 (p0) REVERT: W 176 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8810 (t80) REVERT: Y 261 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8382 (p90) outliers start: 28 outliers final: 20 residues processed: 94 average time/residue: 0.1847 time to fit residues: 26.5323 Evaluate side-chains 93 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain W residue 37 ASN Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 118 ARG Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain X residue 393 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 27 optimal weight: 0.0060 chunk 102 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 87 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.073087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.055361 restraints weight = 32221.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.057202 restraints weight = 16921.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.058444 restraints weight = 11400.323| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9668 Z= 0.136 Angle : 0.581 10.562 13172 Z= 0.279 Chirality : 0.044 0.157 1572 Planarity : 0.003 0.035 1702 Dihedral : 4.997 72.540 1433 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.46 % Allowed : 26.09 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.46 (0.25), residues: 1296 helix: 3.00 (0.26), residues: 411 sheet: -1.31 (0.34), residues: 234 loop : -0.87 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 355 HIS 0.002 0.000 HIS J 79 PHE 0.009 0.001 PHE W 83 TYR 0.007 0.001 TYR Y 32 ARG 0.002 0.000 ARG U 156 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 366) hydrogen bonds : angle 3.46890 ( 1059) metal coordination : bond 0.00639 ( 12) metal coordination : angle 2.94842 ( 18) covalent geometry : bond 0.00318 ( 9656) covalent geometry : angle 0.57143 (13154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3452.79 seconds wall clock time: 61 minutes 51.22 seconds (3711.22 seconds total)