Starting phenix.real_space_refine on Wed Sep 17 16:00:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pr4_17834/09_2025/8pr4_17834.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pr4_17834/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8pr4_17834/09_2025/8pr4_17834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pr4_17834/09_2025/8pr4_17834.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pr4_17834/09_2025/8pr4_17834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pr4_17834/09_2025/8pr4_17834.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ASP:plan': 1, 'ASN:plan1': 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: {'HIS:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLU: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: {'ASN:plan1': 1, 'ASP:plan': 5, 'ARG:plan': 3, 'GLU: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: {'GLU:plan': 14, 'ASP:plan': 11, 'ARG:plan': 2, 'ASN:plan1': 4, 'GLN:plan1': 3, 'HIS:plan': 1, 'PHE: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: {'GLU:plan': 13, 'PHE:plan': 4, 'ARG:plan': 10, 'ASP:plan': 4, 'ASN:plan1': 6, 'GLN:plan1': 7, 'TYR:plan': 1, 'TRP:plan': 1} 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: {'ARG:plan': 10, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 12, 'ASN:plan1': 6, 'GLN:plan1': 7, 'TYR:plan': 1, 'TRP:plan': 1} 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: 2.33, per 1000 atoms: 0.25 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: 0.74 Conformation dependent library (CDL) restraints added in 382.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.40 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: 1.51 Time building geometry restraints manager: 1.02 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: 6.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.023 0.001 ARG U 156 TYR 0.018 0.002 TYR J 76 PHE 0.029 0.002 PHE W 83 TRP 0.069 0.005 TRP J 387 HIS 0.007 0.001 HIS W 90 Details of bonding type rmsd covalent geometry : bond 0.00833 ( 9656) covalent geometry : angle 1.33090 (13154) hydrogen bonds : bond 0.13780 ( 366) hydrogen bonds : angle 7.19128 ( 1059) metal coordination : bond 0.00822 ( 12) metal coordination : angle 6.50174 ( 18) *********************** 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 : 0.355 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: 0.0863 time to fit residues: 12.2035 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 : 0.404 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 351 ASN Y 138 HIS Y 253 GLN X 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.075227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.057008 restraints weight = 31595.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058906 restraints weight = 16488.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060198 restraints weight = 11039.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061027 restraints weight = 8545.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.061479 restraints weight = 7259.426| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9668 Z= 0.189 Angle : 0.653 13.291 13172 Z= 0.323 Chirality : 0.045 0.139 1572 Planarity : 0.006 0.071 1702 Dihedral : 6.567 68.908 1435 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.01 % Allowed : 25.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.22), residues: 1296 helix: 0.06 (0.25), residues: 403 sheet: -1.29 (0.38), residues: 189 loop : -1.79 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 156 TYR 0.009 0.001 TYR Y 240 PHE 0.009 0.001 PHE Y 296 TRP 0.026 0.002 TRP J 387 HIS 0.003 0.001 HIS Y 430 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9656) covalent geometry : angle 0.63525 (13154) hydrogen bonds : bond 0.03875 ( 366) hydrogen bonds : angle 4.47820 ( 1059) metal coordination : bond 0.00890 ( 12) metal coordination : angle 4.12944 ( 18) *********************** 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 110 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7611 (t80) REVERT: J 365 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7323 (mt0) REVERT: U 123 CYS cc_start: 0.8674 (p) cc_final: 0.8333 (m) REVERT: W 37 ASN cc_start: 0.7340 (OUTLIER) cc_final: 0.7004 (p0) REVERT: Y 253 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8566 (tp-100) REVERT: Y 261 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8329 (p90) REVERT: Y 319 MET cc_start: 0.8437 (pmm) cc_final: 0.8003 (pmm) outliers start: 36 outliers final: 14 residues processed: 104 average time/residue: 0.0836 time to fit residues: 13.2527 Evaluate side-chains 85 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 148 CYS Chi-restraints excluded: chain W residue 37 ASN 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 87 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 275 ASN J 380 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.074635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.056579 restraints weight = 31566.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.058443 restraints weight = 16399.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.059736 restraints weight = 10988.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.060539 restraints weight = 8476.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061106 restraints weight = 7202.553| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1734 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= 0.177 Angle : 0.614 11.585 13172 Z= 0.300 Chirality : 0.044 0.147 1572 Planarity : 0.005 0.042 1702 Dihedral : 5.965 72.626 1433 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.79 % Allowed : 23.97 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.24), residues: 1296 helix: 1.38 (0.27), residues: 403 sheet: -1.55 (0.35), residues: 224 loop : -1.49 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 317 TYR 0.008 0.001 TYR Y 32 PHE 0.008 0.001 PHE U 134 TRP 0.016 0.002 TRP J 387 HIS 0.002 0.001 HIS U 36 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9656) covalent geometry : angle 0.60001 (13154) hydrogen bonds : bond 0.03395 ( 366) hydrogen bonds : angle 4.13623 ( 1059) metal coordination : bond 0.00843 ( 12) metal coordination : angle 3.51665 ( 18) *********************** 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 112 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 69 time to evaluate : 0.392 Fit side-chains REVERT: J 76 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7728 (t80) REVERT: J 365 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7284 (mt0) REVERT: J 380 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7969 (pp30) REVERT: U 125 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8778 (mp) REVERT: W 176 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8863 (t80) REVERT: Y 261 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8325 (p90) REVERT: Y 319 MET cc_start: 0.8215 (pmm) cc_final: 0.7900 (pmm) REVERT: X 380 ASP cc_start: 0.7892 (t0) cc_final: 0.7673 (t0) outliers start: 43 outliers final: 26 residues processed: 107 average time/residue: 0.0838 time to fit residues: 13.6181 Evaluate side-chains 97 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 171 LEU 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 275 ASN 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 85 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 152 LEU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.074435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.056403 restraints weight = 31860.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.058296 restraints weight = 16561.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.059567 restraints weight = 11063.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.060375 restraints weight = 8553.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.060956 restraints weight = 7274.642| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9668 Z= 0.160 Angle : 0.592 10.671 13172 Z= 0.287 Chirality : 0.044 0.146 1572 Planarity : 0.004 0.040 1702 Dihedral : 5.704 74.014 1433 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.24), residues: 1296 helix: 1.93 (0.27), residues: 410 sheet: -1.57 (0.35), residues: 218 loop : -1.36 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 317 TYR 0.008 0.001 TYR Y 32 PHE 0.008 0.001 PHE U 134 TRP 0.012 0.001 TRP J 387 HIS 0.002 0.001 HIS U 36 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9656) covalent geometry : angle 0.57939 (13154) hydrogen bonds : bond 0.03212 ( 366) hydrogen bonds : angle 3.93147 ( 1059) metal coordination : bond 0.00756 ( 12) metal coordination : angle 3.27590 ( 18) *********************** 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 111 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7807 (t80) REVERT: J 137 MET cc_start: 0.7979 (tpp) cc_final: 0.7708 (tpp) REVERT: J 365 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7326 (mt0) REVERT: U 125 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8774 (mp) REVERT: W 37 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.7206 (p0) REVERT: W 162 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7957 (tp40) REVERT: W 176 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8887 (t80) REVERT: Y 261 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.8326 (p90) REVERT: Y 319 MET cc_start: 0.8139 (pmm) cc_final: 0.7887 (pmm) outliers start: 46 outliers final: 26 residues processed: 106 average time/residue: 0.0833 time to fit residues: 13.3554 Evaluate side-chains 95 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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 W residue 1 MET 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 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 152 LEU 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 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 107 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.071999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.054305 restraints weight = 32569.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.056079 restraints weight = 17218.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.057255 restraints weight = 11656.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.058085 restraints weight = 9075.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.058614 restraints weight = 7683.809| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9668 Z= 0.179 Angle : 0.595 9.980 13172 Z= 0.291 Chirality : 0.044 0.156 1572 Planarity : 0.004 0.038 1702 Dihedral : 5.563 73.618 1433 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.02 % Allowed : 23.97 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.25), residues: 1296 helix: 2.25 (0.27), residues: 415 sheet: -1.62 (0.36), residues: 208 loop : -1.20 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 156 TYR 0.007 0.001 TYR Y 32 PHE 0.008 0.001 PHE Y 74 TRP 0.010 0.001 TRP J 387 HIS 0.002 0.001 HIS U 36 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9656) covalent geometry : angle 0.58319 (13154) hydrogen bonds : bond 0.03209 ( 366) hydrogen bonds : angle 3.78371 ( 1059) metal coordination : bond 0.00872 ( 12) metal coordination : angle 3.25155 ( 18) *********************** 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: 45 poor density : 65 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.7920 (t80) REVERT: J 126 MET cc_start: 0.8966 (mtm) cc_final: 0.8411 (mtm) REVERT: J 137 MET cc_start: 0.7834 (tpp) cc_final: 0.7552 (tpp) REVERT: J 365 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7302 (mt0) REVERT: U 125 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8750 (mp) REVERT: W 37 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.7262 (p0) REVERT: W 162 GLN cc_start: 0.8263 (tp-100) cc_final: 0.8036 (tp40) REVERT: W 176 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8801 (t80) REVERT: Y 261 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8300 (p90) outliers start: 45 outliers final: 28 residues processed: 106 average time/residue: 0.0812 time to fit residues: 12.9761 Evaluate side-chains 97 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 1 MET 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 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 152 LEU 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 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 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 35 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.071052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.053351 restraints weight = 32515.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055093 restraints weight = 17282.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.056310 restraints weight = 11737.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.057114 restraints weight = 9153.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.057576 restraints weight = 7770.609| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9668 Z= 0.223 Angle : 0.633 11.262 13172 Z= 0.309 Chirality : 0.045 0.153 1572 Planarity : 0.004 0.036 1702 Dihedral : 5.659 72.923 1433 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.69 % Allowed : 23.52 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.25), residues: 1296 helix: 2.32 (0.27), residues: 416 sheet: -1.64 (0.34), residues: 219 loop : -1.23 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 156 TYR 0.008 0.001 TYR J 112 PHE 0.010 0.001 PHE Y 296 TRP 0.010 0.001 TRP J 355 HIS 0.002 0.001 HIS W 60 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 9656) covalent geometry : angle 0.61922 (13154) hydrogen bonds : bond 0.03306 ( 366) hydrogen bonds : angle 3.83945 ( 1059) metal coordination : bond 0.00981 ( 12) metal coordination : angle 3.59628 ( 18) *********************** 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 117 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 66 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8084 (t80) REVERT: J 126 MET cc_start: 0.8916 (mtm) cc_final: 0.8308 (mtt) REVERT: J 137 MET cc_start: 0.7826 (tpp) cc_final: 0.7500 (tpp) REVERT: J 365 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7362 (mt0) REVERT: J 387 TRP cc_start: 0.8428 (p-90) cc_final: 0.6557 (m100) REVERT: U 125 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8707 (mp) REVERT: W 37 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7289 (p0) REVERT: W 176 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8747 (t80) REVERT: Y 261 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8271 (p90) outliers start: 51 outliers final: 30 residues processed: 113 average time/residue: 0.0909 time to fit residues: 15.0487 Evaluate side-chains 99 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 63 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 115 VAL Chi-restraints excluded: chain J residue 118 VAL 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 1 MET Chi-restraints excluded: chain W residue 28 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 85 LEU 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 82 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.071986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.054228 restraints weight = 32548.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.056046 restraints weight = 17177.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.057237 restraints weight = 11593.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.058038 restraints weight = 9048.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.058529 restraints weight = 7690.011| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9668 Z= 0.155 Angle : 0.583 9.636 13172 Z= 0.284 Chirality : 0.044 0.152 1572 Planarity : 0.004 0.036 1702 Dihedral : 5.427 74.166 1433 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.24 % Allowed : 24.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.25), residues: 1296 helix: 2.56 (0.27), residues: 416 sheet: -1.55 (0.35), residues: 219 loop : -1.15 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 102 TYR 0.008 0.001 TYR Y 12 PHE 0.008 0.001 PHE U 134 TRP 0.011 0.001 TRP J 355 HIS 0.002 0.001 HIS J 79 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9656) covalent geometry : angle 0.56989 (13154) hydrogen bonds : bond 0.03062 ( 366) hydrogen bonds : angle 3.67135 ( 1059) metal coordination : bond 0.00768 ( 12) metal coordination : angle 3.34179 ( 18) *********************** 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 117 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 70 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8042 (t80) REVERT: J 126 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8226 (mtm) REVERT: J 137 MET cc_start: 0.7665 (tpp) cc_final: 0.7353 (tpp) REVERT: J 365 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7334 (mt0) REVERT: J 387 TRP cc_start: 0.8431 (p-90) cc_final: 0.6519 (m100) REVERT: U 125 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8688 (mp) REVERT: W 37 ASN cc_start: 0.7572 (OUTLIER) cc_final: 0.7224 (p0) REVERT: W 176 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8753 (t80) REVERT: Y 261 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8269 (p90) REVERT: Y 268 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8312 (mm-40) REVERT: Y 319 MET cc_start: 0.8188 (pmm) cc_final: 0.7800 (pmm) outliers start: 47 outliers final: 31 residues processed: 112 average time/residue: 0.0875 time to fit residues: 14.6718 Evaluate side-chains 103 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 64 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 126 MET Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 269 ILE 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 1 MET Chi-restraints excluded: chain W residue 3 LEU 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 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 26 GLN 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 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 268 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.072149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.054497 restraints weight = 32178.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.056315 restraints weight = 16940.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.057489 restraints weight = 11420.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.058315 restraints weight = 8921.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.058816 restraints weight = 7564.963| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2669 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= 0.146 Angle : 0.588 10.681 13172 Z= 0.284 Chirality : 0.044 0.143 1572 Planarity : 0.003 0.035 1702 Dihedral : 5.291 74.015 1433 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.02 % Allowed : 24.64 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.25), residues: 1296 helix: 2.68 (0.27), residues: 417 sheet: -1.50 (0.35), residues: 219 loop : -1.11 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 143 TYR 0.007 0.001 TYR Y 32 PHE 0.007 0.001 PHE U 134 TRP 0.011 0.001 TRP J 355 HIS 0.002 0.001 HIS J 79 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9656) covalent geometry : angle 0.57664 (13154) hydrogen bonds : bond 0.03018 ( 366) hydrogen bonds : angle 3.60751 ( 1059) metal coordination : bond 0.00713 ( 12) metal coordination : angle 3.19680 ( 18) *********************** 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 111 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 66 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.7935 (t80) REVERT: J 126 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8118 (mtm) REVERT: J 137 MET cc_start: 0.7568 (tpp) cc_final: 0.7251 (tpp) REVERT: J 365 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7380 (mt0) REVERT: J 387 TRP cc_start: 0.8436 (p-90) cc_final: 0.6495 (m100) REVERT: U 125 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8637 (mp) REVERT: W 37 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.7181 (p0) REVERT: W 176 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8751 (t80) REVERT: Y 261 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8278 (p90) REVERT: Y 268 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8289 (mm-40) REVERT: Y 319 MET cc_start: 0.8180 (pmm) cc_final: 0.7859 (pmm) outliers start: 45 outliers final: 30 residues processed: 106 average time/residue: 0.0859 time to fit residues: 13.6942 Evaluate side-chains 103 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 65 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 126 MET Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 360 ILE 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 1 MET Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 28 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 132 THR Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 26 GLN Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 82 THR 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 268 GLN Chi-restraints excluded: chain Y residue 297 ASN Chi-restraints excluded: chain Y residue 305 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 17 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 18 optimal weight: 0.0570 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.072209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.054460 restraints weight = 32441.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.056279 restraints weight = 17089.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.057490 restraints weight = 11541.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058281 restraints weight = 8976.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.058800 restraints weight = 7645.084| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9668 Z= 0.152 Angle : 0.580 9.289 13172 Z= 0.282 Chirality : 0.044 0.142 1572 Planarity : 0.004 0.034 1702 Dihedral : 5.223 74.236 1433 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.35 % Allowed : 24.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.25), residues: 1296 helix: 2.75 (0.26), residues: 417 sheet: -1.49 (0.35), residues: 219 loop : -1.07 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 156 TYR 0.007 0.001 TYR J 112 PHE 0.007 0.001 PHE Y 296 TRP 0.010 0.001 TRP J 355 HIS 0.002 0.001 HIS J 79 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9656) covalent geometry : angle 0.56834 (13154) hydrogen bonds : bond 0.03010 ( 366) hydrogen bonds : angle 3.56626 ( 1059) metal coordination : bond 0.00748 ( 12) metal coordination : angle 3.24544 ( 18) *********************** 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 115 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 67 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.7944 (t80) REVERT: J 126 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8104 (mtm) REVERT: J 137 MET cc_start: 0.7522 (tpp) cc_final: 0.7185 (tpp) REVERT: J 365 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7380 (mt0) REVERT: J 387 TRP cc_start: 0.8469 (p-90) cc_final: 0.6490 (m100) REVERT: U 125 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8633 (mp) REVERT: W 37 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.7170 (p0) REVERT: W 176 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8758 (t80) REVERT: Y 261 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8290 (p90) REVERT: Y 268 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8298 (mm-40) REVERT: Y 319 MET cc_start: 0.8185 (pmm) cc_final: 0.7858 (pmm) outliers start: 48 outliers final: 31 residues processed: 110 average time/residue: 0.0812 time to fit residues: 13.2857 Evaluate side-chains 102 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 63 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 115 VAL Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 360 ILE 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 1 MET Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 28 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 132 THR Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 26 GLN Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 82 THR 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 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 268 GLN 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 43 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 101 optimal weight: 0.0000 chunk 68 optimal weight: 0.6980 chunk 85 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 2 optimal weight: 0.0270 chunk 22 optimal weight: 0.0270 chunk 3 optimal weight: 0.9980 overall best weight: 0.3300 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.074035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.056241 restraints weight = 31952.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.058093 restraints weight = 17110.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.059270 restraints weight = 11598.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060126 restraints weight = 9115.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.060636 restraints weight = 7740.218| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2755 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= 0.099 Angle : 0.569 9.960 13172 Z= 0.275 Chirality : 0.043 0.148 1572 Planarity : 0.003 0.034 1702 Dihedral : 4.930 72.965 1433 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.90 % Allowed : 26.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.25), residues: 1296 helix: 3.01 (0.26), residues: 410 sheet: -1.31 (0.35), residues: 230 loop : -0.91 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 156 TYR 0.009 0.001 TYR Y 32 PHE 0.007 0.001 PHE U 134 TRP 0.013 0.001 TRP J 355 HIS 0.007 0.001 HIS W 109 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9656) covalent geometry : angle 0.55769 (13154) hydrogen bonds : bond 0.02712 ( 366) hydrogen bonds : angle 3.41693 ( 1059) metal coordination : bond 0.00500 ( 12) metal coordination : angle 3.11636 ( 18) ********************** 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 100 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.7972 (t80) REVERT: J 126 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8164 (mtm) REVERT: J 137 MET cc_start: 0.7442 (tpp) cc_final: 0.7190 (tpp) REVERT: J 365 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7344 (mt0) REVERT: J 387 TRP cc_start: 0.8438 (p-90) cc_final: 0.6459 (m100) REVERT: U 125 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8593 (mp) REVERT: W 37 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6929 (p0) REVERT: Y 261 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8507 (p90) REVERT: Y 319 MET cc_start: 0.8221 (pmm) cc_final: 0.7954 (pmm) outliers start: 26 outliers final: 18 residues processed: 97 average time/residue: 0.0775 time to fit residues: 11.4064 Evaluate side-chains 91 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 126 MET 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 1 MET Chi-restraints excluded: chain W residue 37 ASN Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 132 THR 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 56 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 64 ASN U 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.070500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.052751 restraints weight = 32675.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.054491 restraints weight = 17442.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055685 restraints weight = 11901.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.056423 restraints weight = 9289.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.056791 restraints weight = 7962.497| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9668 Z= 0.307 Angle : 0.694 9.784 13172 Z= 0.342 Chirality : 0.047 0.140 1572 Planarity : 0.004 0.034 1702 Dihedral : 5.515 71.442 1433 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.01 % Allowed : 25.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.25), residues: 1296 helix: 2.63 (0.26), residues: 413 sheet: -1.70 (0.34), residues: 219 loop : -1.16 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG Y 255 TYR 0.016 0.001 TYR U 144 PHE 0.012 0.001 PHE Y 296 TRP 0.009 0.002 TRP Y 133 HIS 0.006 0.001 HIS W 109 Details of bonding type rmsd covalent geometry : bond 0.00700 ( 9656) covalent geometry : angle 0.68006 (13154) hydrogen bonds : bond 0.03476 ( 366) hydrogen bonds : angle 3.78242 ( 1059) metal coordination : bond 0.01204 ( 12) metal coordination : angle 3.78786 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1807.26 seconds wall clock time: 31 minutes 56.04 seconds (1916.04 seconds total)