Starting phenix.real_space_refine on Fri May 16 10:27:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thb_41252/05_2025/8thb_41252.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thb_41252/05_2025/8thb_41252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8thb_41252/05_2025/8thb_41252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thb_41252/05_2025/8thb_41252.map" model { file = "/net/cci-nas-00/data/ceres_data/8thb_41252/05_2025/8thb_41252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thb_41252/05_2025/8thb_41252.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 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 P 14 5.49 5 Mg 3 5.21 5 S 68 5.16 5 C 9029 2.51 5 N 2481 2.21 5 O 2739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14334 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3810 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 21, 'TRANS': 446} Chain breaks: 4 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2495 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2571 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2629 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2675 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.26, per 1000 atoms: 0.58 Number of scatterers: 14334 At special positions: 0 Unit cell: (100.188, 121.716, 120.06, 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) S 68 16.00 P 14 15.00 Mg 3 11.99 O 2739 8.00 N 2481 7.00 C 9029 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: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3428 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 8 sheets defined 62.4% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.505A pdb=" N TYR A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 256 through 274 removed outlier: 3.579A pdb=" N ARG A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.570A pdb=" N ALA A 355 " --> pdb=" O MET A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 387 removed outlier: 5.400A pdb=" N ASP A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 429 Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.685A pdb=" N LEU A 480 " --> pdb=" O TYR A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.572A pdb=" N PHE A 509 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 510 " --> pdb=" O HIS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 557 removed outlier: 3.651A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 585 through 590 Processing helix chain 'A' and resid 616 through 627 removed outlier: 4.182A pdb=" N HIS A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 637 removed outlier: 4.035A pdb=" N ARG A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 659 Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.665A pdb=" N LEU A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 716 Processing helix chain 'A' and resid 716 through 731 removed outlier: 3.660A pdb=" N GLU A 723 " --> pdb=" O PRO A 719 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 780 removed outlier: 3.606A pdb=" N VAL A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.653A pdb=" N VAL B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.915A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.504A pdb=" N TYR B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 276 removed outlier: 3.627A pdb=" N ASN B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.661A pdb=" N LEU B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 323 removed outlier: 3.777A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.504A pdb=" N THR C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 removed outlier: 3.562A pdb=" N ILE C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.816A pdb=" N ARG C 94 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.828A pdb=" N ALA C 121 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 170 through 183 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.684A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.515A pdb=" N ILE C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.933A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 334 removed outlier: 3.775A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 3.606A pdb=" N TYR D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 56 removed outlier: 3.596A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 84 through 92 removed outlier: 3.688A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.557A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.622A pdb=" N ALA D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 removed outlier: 3.694A pdb=" N LYS D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.623A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.639A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.705A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.160A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.609A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 178 through 184 removed outlier: 3.514A pdb=" N ARG E 184 " --> pdb=" O PRO E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.552A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 4.000A pdb=" N LEU E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.206A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 removed outlier: 3.931A pdb=" N VAL A 227 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 366 removed outlier: 3.725A pdb=" N LEU A 402 " --> pdb=" O GLN A 362 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET A 334 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE A 335 " --> pdb=" O PHE A 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 600 through 601 removed outlier: 6.492A pdb=" N LEU A 600 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP E 71 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.058A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 83 removed outlier: 5.843A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 63 through 64 removed outlier: 3.739A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 135 through 140 removed outlier: 3.811A pdb=" N LEU D 139 " --> pdb=" O CYS D 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.154A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 731 hydrogen bonds defined for protein. 2154 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: 3.88 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 4750 1.35 - 1.50: 3482 1.50 - 1.65: 6234 1.65 - 1.80: 39 1.80 - 1.95: 65 Bond restraints: 14570 Sorted by residual: bond pdb=" N ASP D 178 " pdb=" CA ASP D 178 " ideal model delta sigma weight residual 1.462 1.491 -0.029 8.50e-03 1.38e+04 1.17e+01 bond pdb=" C PRO A 196 " pdb=" O PRO A 196 " ideal model delta sigma weight residual 1.243 1.216 0.027 8.50e-03 1.38e+04 1.04e+01 bond pdb=" N ILE D 177 " pdb=" CA ILE D 177 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.25e-02 6.40e+03 9.77e+00 bond pdb=" C PRO D 132 " pdb=" O PRO D 132 " ideal model delta sigma weight residual 1.240 1.206 0.035 1.12e-02 7.97e+03 9.65e+00 bond pdb=" N TYR D 134 " pdb=" CA TYR D 134 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.22e-02 6.72e+03 8.25e+00 ... (remaining 14565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 19424 1.91 - 3.82: 262 3.82 - 5.73: 43 5.73 - 7.64: 7 7.64 - 9.54: 3 Bond angle restraints: 19739 Sorted by residual: angle pdb=" CA PRO D 179 " pdb=" C PRO D 179 " pdb=" O PRO D 179 " ideal model delta sigma weight residual 121.56 116.75 4.81 1.16e+00 7.43e-01 1.72e+01 angle pdb=" N PRO D 132 " pdb=" CA PRO D 132 " pdb=" C PRO D 132 " ideal model delta sigma weight residual 110.70 106.45 4.25 1.22e+00 6.72e-01 1.21e+01 angle pdb=" C ASP C 87 " pdb=" CA ASP C 87 " pdb=" CB ASP C 87 " ideal model delta sigma weight residual 110.67 115.51 -4.84 1.52e+00 4.33e-01 1.01e+01 angle pdb=" CA ALA D 181 " pdb=" C ALA D 181 " pdb=" O ALA D 181 " ideal model delta sigma weight residual 122.38 117.74 4.64 1.49e+00 4.50e-01 9.70e+00 angle pdb=" C MET A 334 " pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta sigma weight residual 123.12 119.09 4.03 1.30e+00 5.92e-01 9.62e+00 ... (remaining 19734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.37: 7953 19.37 - 38.75: 828 38.75 - 58.12: 170 58.12 - 77.50: 52 77.50 - 96.87: 5 Dihedral angle restraints: 9008 sinusoidal: 3757 harmonic: 5251 Sorted by residual: dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 29.14 -96.87 1 3.00e+01 1.11e-03 1.19e+01 dihedral pdb=" CG ARG B 272 " pdb=" CD ARG B 272 " pdb=" NE ARG B 272 " pdb=" CZ ARG B 272 " ideal model delta sinusoidal sigma weight residual 90.00 134.80 -44.80 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ASN D 196 " pdb=" CB ASN D 196 " pdb=" CG ASN D 196 " pdb=" OD1 ASN D 196 " ideal model delta sinusoidal sigma weight residual 120.00 -170.54 -69.46 2 2.00e+01 2.50e-03 1.05e+01 ... (remaining 9005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1798 0.043 - 0.086: 387 0.086 - 0.128: 110 0.128 - 0.171: 14 0.171 - 0.214: 3 Chirality restraints: 2312 Sorted by residual: chirality pdb=" CA ILE D 176 " pdb=" N ILE D 176 " pdb=" C ILE D 176 " pdb=" CB ILE D 176 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA MET A 334 " pdb=" N MET A 334 " pdb=" C MET A 334 " pdb=" CB MET A 334 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CB ILE A 219 " pdb=" CA ILE A 219 " pdb=" CG1 ILE A 219 " pdb=" CG2 ILE A 219 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 2309 not shown) Planarity restraints: 2488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 780 " 0.023 2.00e-02 2.50e+03 2.99e-02 2.23e+01 pdb=" CG TRP A 780 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP A 780 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP A 780 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 780 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 780 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 780 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 780 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 780 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 780 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 266 " 0.016 2.00e-02 2.50e+03 2.51e-02 1.58e+01 pdb=" CG TRP A 266 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 266 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP A 266 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 266 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 266 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 266 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 266 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 266 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 266 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 97 " -0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO E 98 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " -0.045 5.00e-02 4.00e+02 ... (remaining 2485 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 754 2.73 - 3.28: 14825 3.28 - 3.82: 23590 3.82 - 4.36: 28938 4.36 - 4.90: 49053 Nonbonded interactions: 117160 Sorted by model distance: nonbonded pdb=" OD2 ASP D 140 " pdb="MG MG D 402 " model vdw 2.192 2.170 nonbonded pdb=" OD1 ASP B 229 " pdb=" OH TYR C 52 " model vdw 2.249 3.040 nonbonded pdb=" OG SER C 228 " pdb=" OD1 ASP C 230 " model vdw 2.259 3.040 nonbonded pdb=" O GLU A 574 " pdb=" OG1 THR A 578 " model vdw 2.259 3.040 nonbonded pdb=" O VAL E 5 " pdb=" O3' ADP E 401 " model vdw 2.263 3.040 ... (remaining 117155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 31.150 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.003 0.039 14570 Z= 0.159 Angle : 0.549 9.544 19739 Z= 0.301 Chirality : 0.040 0.214 2312 Planarity : 0.005 0.094 2488 Dihedral : 16.451 96.869 5580 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.37 % Allowed : 20.10 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 1762 helix: 0.51 (0.15), residues: 992 sheet: -0.03 (0.44), residues: 154 loop : -0.31 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP A 780 HIS 0.005 0.001 HIS A 415 PHE 0.006 0.001 PHE A 592 TYR 0.026 0.001 TYR D 129 ARG 0.015 0.000 ARG A 647 Details of bonding type rmsd hydrogen bonds : bond 0.24532 ( 731) hydrogen bonds : angle 7.11664 ( 2154) covalent geometry : bond 0.00264 (14570) covalent geometry : angle 0.54903 (19739) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 197 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 129 TYR cc_start: 0.7556 (m-10) cc_final: 0.7309 (m-10) outliers start: 6 outliers final: 2 residues processed: 199 average time/residue: 0.2515 time to fit residues: 75.0077 Evaluate side-chains 192 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 480 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 0.0370 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 0.0070 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN B 208 ASN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 35 ASN D 171 ASN E 104 ASN E 164 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.149829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112132 restraints weight = 20577.615| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.51 r_work: 0.3221 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14570 Z= 0.143 Angle : 0.539 8.930 19739 Z= 0.281 Chirality : 0.040 0.148 2312 Planarity : 0.004 0.071 2488 Dihedral : 8.111 95.059 2013 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.24 % Allowed : 17.55 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1762 helix: 1.28 (0.16), residues: 1027 sheet: -0.28 (0.42), residues: 157 loop : -0.10 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 266 HIS 0.006 0.001 HIS A 415 PHE 0.014 0.001 PHE E 328 TYR 0.017 0.001 TYR D 286 ARG 0.004 0.001 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 731) hydrogen bonds : angle 4.62032 ( 2154) covalent geometry : bond 0.00319 (14570) covalent geometry : angle 0.53917 (19739) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 588 MET cc_start: 0.7564 (mtt) cc_final: 0.7364 (mtp) REVERT: B 45 MET cc_start: 0.8762 (mtm) cc_final: 0.8396 (mtm) REVERT: B 199 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: B 255 ASP cc_start: 0.8965 (m-30) cc_final: 0.8635 (m-30) REVERT: C 98 LYS cc_start: 0.8000 (ptmt) cc_final: 0.7672 (pttp) REVERT: D 51 LYS cc_start: 0.8202 (mttt) cc_final: 0.7497 (mtmm) REVERT: D 154 ARG cc_start: 0.7520 (tpt90) cc_final: 0.6877 (tpt90) REVERT: E 83 LEU cc_start: 0.7928 (tt) cc_final: 0.7679 (tt) REVERT: E 111 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7792 (tm-30) outliers start: 36 outliers final: 15 residues processed: 233 average time/residue: 0.2717 time to fit residues: 93.1547 Evaluate side-chains 211 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 261 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 36 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 12 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 166 optimal weight: 0.0070 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107986 restraints weight = 20720.829| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.51 r_work: 0.3164 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14570 Z= 0.173 Angle : 0.538 9.951 19739 Z= 0.273 Chirality : 0.041 0.140 2312 Planarity : 0.004 0.072 2488 Dihedral : 7.673 86.127 2011 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.99 % Allowed : 16.68 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1762 helix: 1.41 (0.16), residues: 1020 sheet: -0.36 (0.40), residues: 157 loop : 0.07 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 266 HIS 0.004 0.001 HIS B 44 PHE 0.018 0.001 PHE E 305 TYR 0.020 0.002 TYR A 361 ARG 0.004 0.001 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 731) hydrogen bonds : angle 4.36958 ( 2154) covalent geometry : bond 0.00411 (14570) covalent geometry : angle 0.53773 (19739) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 TYR cc_start: 0.8508 (p90) cc_final: 0.8293 (p90) REVERT: A 588 MET cc_start: 0.7607 (mtt) cc_final: 0.7401 (mtp) REVERT: C 98 LYS cc_start: 0.7981 (ptmt) cc_final: 0.7652 (pttp) REVERT: D 51 LYS cc_start: 0.8155 (mttt) cc_final: 0.7463 (mtmm) REVERT: D 154 ARG cc_start: 0.7572 (tpt90) cc_final: 0.6894 (tpt90) REVERT: D 165 ARG cc_start: 0.4738 (OUTLIER) cc_final: 0.4170 (tpm170) outliers start: 48 outliers final: 26 residues processed: 234 average time/residue: 0.2583 time to fit residues: 89.3677 Evaluate side-chains 210 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 261 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 166 optimal weight: 0.0020 chunk 109 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 HIS B 250 GLN C 83 ASN D 35 ASN D 196 ASN E 164 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.143192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104857 restraints weight = 20700.657| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.51 r_work: 0.3112 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14570 Z= 0.234 Angle : 0.587 10.828 19739 Z= 0.297 Chirality : 0.043 0.154 2312 Planarity : 0.004 0.071 2488 Dihedral : 7.667 84.276 2011 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.11 % Allowed : 16.43 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1762 helix: 1.26 (0.16), residues: 1021 sheet: -0.58 (0.39), residues: 157 loop : 0.01 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 266 HIS 0.010 0.001 HIS B 317 PHE 0.021 0.002 PHE E 305 TYR 0.022 0.002 TYR D 286 ARG 0.005 0.001 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 731) hydrogen bonds : angle 4.41987 ( 2154) covalent geometry : bond 0.00568 (14570) covalent geometry : angle 0.58696 (19739) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 198 time to evaluate : 1.673 Fit side-chains revert: symmetry clash REVERT: A 361 TYR cc_start: 0.8565 (p90) cc_final: 0.8329 (p90) REVERT: A 406 ASN cc_start: 0.9026 (t0) cc_final: 0.8524 (m110) REVERT: A 588 MET cc_start: 0.7611 (mtt) cc_final: 0.7359 (mtp) REVERT: B 250 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: C 98 LYS cc_start: 0.7939 (ptmt) cc_final: 0.7600 (pttp) REVERT: D 51 LYS cc_start: 0.8277 (mttt) cc_final: 0.7601 (mtmm) REVERT: D 134 TYR cc_start: 0.6588 (p90) cc_final: 0.5719 (p90) REVERT: D 154 ARG cc_start: 0.7561 (tpt90) cc_final: 0.7006 (tpt90) REVERT: D 165 ARG cc_start: 0.4760 (OUTLIER) cc_final: 0.4131 (tpm170) REVERT: E 8 TYR cc_start: 0.7715 (m-10) cc_final: 0.7064 (m-10) REVERT: E 255 ILE cc_start: 0.8591 (mm) cc_final: 0.8176 (mt) REVERT: E 266 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8509 (tt) outliers start: 66 outliers final: 42 residues processed: 246 average time/residue: 0.2546 time to fit residues: 93.0545 Evaluate side-chains 230 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 143 optimal weight: 0.7980 chunk 151 optimal weight: 0.0370 chunk 2 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 GLN D 35 ASN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.145897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110706 restraints weight = 20771.033| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.33 r_work: 0.3168 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14570 Z= 0.113 Angle : 0.506 9.384 19739 Z= 0.256 Chirality : 0.039 0.153 2312 Planarity : 0.004 0.071 2488 Dihedral : 7.430 83.331 2011 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 3.17 % Allowed : 17.80 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1762 helix: 1.57 (0.16), residues: 1013 sheet: -0.48 (0.39), residues: 150 loop : 0.07 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 266 HIS 0.005 0.001 HIS B 317 PHE 0.010 0.001 PHE E 328 TYR 0.019 0.001 TYR D 64 ARG 0.005 0.000 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 731) hydrogen bonds : angle 4.16583 ( 2154) covalent geometry : bond 0.00252 (14570) covalent geometry : angle 0.50586 (19739) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 TRP cc_start: 0.8050 (t60) cc_final: 0.7757 (t60) REVERT: A 361 TYR cc_start: 0.8489 (p90) cc_final: 0.8213 (p90) REVERT: A 406 ASN cc_start: 0.8916 (t0) cc_final: 0.8391 (m110) REVERT: A 549 ASN cc_start: 0.9332 (t0) cc_final: 0.9086 (t0) REVERT: A 588 MET cc_start: 0.7733 (mtt) cc_final: 0.7437 (mtp) REVERT: C 98 LYS cc_start: 0.7898 (ptmt) cc_final: 0.7588 (pttp) REVERT: C 199 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: D 38 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: D 51 LYS cc_start: 0.8258 (mttt) cc_final: 0.7544 (mtmm) REVERT: D 154 ARG cc_start: 0.7503 (tpt90) cc_final: 0.6825 (tpt90) REVERT: D 189 PHE cc_start: 0.7994 (m-10) cc_final: 0.7786 (m-10) REVERT: E 8 TYR cc_start: 0.7682 (m-10) cc_final: 0.7206 (m-10) REVERT: E 66 TYR cc_start: 0.9015 (m-80) cc_final: 0.8705 (m-80) REVERT: E 255 ILE cc_start: 0.8598 (mm) cc_final: 0.8218 (mt) REVERT: E 266 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8522 (tt) outliers start: 51 outliers final: 29 residues processed: 244 average time/residue: 0.2415 time to fit residues: 88.3596 Evaluate side-chains 230 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 99 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 104 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN E 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.146155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107397 restraints weight = 21048.086| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.59 r_work: 0.3153 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14570 Z= 0.125 Angle : 0.501 8.647 19739 Z= 0.252 Chirality : 0.040 0.150 2312 Planarity : 0.004 0.071 2488 Dihedral : 7.330 82.375 2011 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 2.92 % Allowed : 18.11 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1762 helix: 1.65 (0.16), residues: 1014 sheet: -0.45 (0.40), residues: 150 loop : 0.07 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 266 HIS 0.003 0.001 HIS B 44 PHE 0.011 0.001 PHE E 305 TYR 0.017 0.001 TYR D 160 ARG 0.005 0.000 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 731) hydrogen bonds : angle 4.07832 ( 2154) covalent geometry : bond 0.00292 (14570) covalent geometry : angle 0.50109 (19739) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 TRP cc_start: 0.8029 (t60) cc_final: 0.7736 (t60) REVERT: A 361 TYR cc_start: 0.8521 (p90) cc_final: 0.8212 (p90) REVERT: A 406 ASN cc_start: 0.8961 (t0) cc_final: 0.8370 (m110) REVERT: A 549 ASN cc_start: 0.9345 (t0) cc_final: 0.9100 (t0) REVERT: A 588 MET cc_start: 0.7572 (mtt) cc_final: 0.7225 (mtp) REVERT: B 255 ASP cc_start: 0.8991 (m-30) cc_final: 0.8626 (m-30) REVERT: C 34 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7287 (pt) REVERT: C 98 LYS cc_start: 0.7908 (ptmt) cc_final: 0.7566 (pttp) REVERT: C 199 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: D 38 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: D 51 LYS cc_start: 0.8202 (mttt) cc_final: 0.7521 (mtmm) REVERT: D 154 ARG cc_start: 0.7514 (tpt90) cc_final: 0.6917 (tpt90) REVERT: D 189 PHE cc_start: 0.8006 (m-10) cc_final: 0.7774 (m-10) REVERT: E 8 TYR cc_start: 0.7709 (m-10) cc_final: 0.7169 (m-10) REVERT: E 255 ILE cc_start: 0.8560 (mm) cc_final: 0.8149 (mt) REVERT: E 266 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8445 (tt) outliers start: 47 outliers final: 32 residues processed: 245 average time/residue: 0.2531 time to fit residues: 92.5669 Evaluate side-chains 231 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 55 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.142300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103740 restraints weight = 21038.011| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.55 r_work: 0.3100 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14570 Z= 0.244 Angle : 0.594 9.350 19739 Z= 0.297 Chirality : 0.043 0.167 2312 Planarity : 0.004 0.072 2488 Dihedral : 7.547 82.406 2011 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 3.67 % Allowed : 17.67 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1762 helix: 1.37 (0.16), residues: 1015 sheet: -0.60 (0.39), residues: 150 loop : -0.06 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 266 HIS 0.006 0.001 HIS B 44 PHE 0.023 0.002 PHE E 305 TYR 0.021 0.002 TYR D 286 ARG 0.004 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 731) hydrogen bonds : angle 4.30043 ( 2154) covalent geometry : bond 0.00593 (14570) covalent geometry : angle 0.59413 (19739) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 195 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 TRP cc_start: 0.8081 (t60) cc_final: 0.7872 (t60) REVERT: A 588 MET cc_start: 0.7557 (mtt) cc_final: 0.7302 (mtp) REVERT: B 115 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8408 (mt-10) REVERT: C 34 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7387 (pt) REVERT: C 118 GLU cc_start: 0.8079 (mt-10) cc_final: 0.6956 (mm-30) REVERT: C 199 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: D 38 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: D 51 LYS cc_start: 0.8225 (mttt) cc_final: 0.7524 (mtmm) REVERT: D 154 ARG cc_start: 0.7555 (tpt90) cc_final: 0.6836 (tpt90) REVERT: E 8 TYR cc_start: 0.7771 (m-10) cc_final: 0.7189 (m-10) REVERT: E 66 TYR cc_start: 0.9113 (m-80) cc_final: 0.8851 (m-80) REVERT: E 266 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8540 (tt) outliers start: 59 outliers final: 37 residues processed: 245 average time/residue: 0.2518 time to fit residues: 91.0454 Evaluate side-chains 229 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 348 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 73 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 138 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.146064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107483 restraints weight = 20855.756| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.57 r_work: 0.3140 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14570 Z= 0.125 Angle : 0.518 11.206 19739 Z= 0.259 Chirality : 0.040 0.197 2312 Planarity : 0.004 0.071 2488 Dihedral : 7.390 81.628 2009 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Rotamer: Outliers : 2.61 % Allowed : 18.61 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.21), residues: 1762 helix: 1.56 (0.16), residues: 1015 sheet: -0.56 (0.40), residues: 150 loop : -0.02 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 266 HIS 0.003 0.001 HIS E 18 PHE 0.029 0.001 PHE A 722 TYR 0.025 0.001 TYR C 71 ARG 0.007 0.000 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 731) hydrogen bonds : angle 4.09724 ( 2154) covalent geometry : bond 0.00292 (14570) covalent geometry : angle 0.51760 (19739) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 TYR cc_start: 0.8308 (p90) cc_final: 0.8038 (p90) REVERT: A 406 ASN cc_start: 0.9060 (t0) cc_final: 0.8476 (m110) REVERT: A 549 ASN cc_start: 0.9366 (t0) cc_final: 0.9135 (t0) REVERT: A 588 MET cc_start: 0.7560 (mtt) cc_final: 0.7289 (mtp) REVERT: A 769 PHE cc_start: 0.4435 (OUTLIER) cc_final: 0.4142 (m-80) REVERT: B 115 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8378 (mt-10) REVERT: B 255 ASP cc_start: 0.9009 (m-30) cc_final: 0.8654 (m-30) REVERT: C 118 GLU cc_start: 0.8113 (mt-10) cc_final: 0.6981 (mm-30) REVERT: C 199 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: D 38 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: D 51 LYS cc_start: 0.8226 (mttt) cc_final: 0.7536 (mtmm) REVERT: D 154 ARG cc_start: 0.7594 (tpt90) cc_final: 0.7005 (tpt90) REVERT: D 189 PHE cc_start: 0.8035 (m-10) cc_final: 0.7727 (m-10) REVERT: E 8 TYR cc_start: 0.7750 (m-10) cc_final: 0.7279 (m-10) REVERT: E 266 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8515 (tt) outliers start: 42 outliers final: 31 residues processed: 228 average time/residue: 0.2406 time to fit residues: 81.9681 Evaluate side-chains 227 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 769 PHE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 93 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 95 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN E 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.146292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107559 restraints weight = 20643.052| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.58 r_work: 0.3146 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14570 Z= 0.123 Angle : 0.514 11.163 19739 Z= 0.255 Chirality : 0.040 0.177 2312 Planarity : 0.004 0.070 2488 Dihedral : 7.321 81.046 2009 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.72 % Favored : 97.22 % Rotamer: Outliers : 2.80 % Allowed : 18.79 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1762 helix: 1.65 (0.17), residues: 1013 sheet: -0.52 (0.40), residues: 150 loop : -0.03 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 266 HIS 0.003 0.001 HIS B 44 PHE 0.022 0.001 PHE A 722 TYR 0.017 0.001 TYR C 71 ARG 0.003 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 731) hydrogen bonds : angle 4.04048 ( 2154) covalent geometry : bond 0.00287 (14570) covalent geometry : angle 0.51435 (19739) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.7275 (m-80) cc_final: 0.7010 (m-80) REVERT: A 361 TYR cc_start: 0.8328 (p90) cc_final: 0.8031 (p90) REVERT: A 406 ASN cc_start: 0.9050 (t0) cc_final: 0.8445 (m110) REVERT: A 549 ASN cc_start: 0.9373 (t0) cc_final: 0.9143 (t0) REVERT: A 588 MET cc_start: 0.7606 (mtt) cc_final: 0.7071 (mtp) REVERT: A 769 PHE cc_start: 0.4414 (OUTLIER) cc_final: 0.4087 (m-80) REVERT: B 255 ASP cc_start: 0.8989 (m-30) cc_final: 0.8649 (m-30) REVERT: C 34 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7355 (pt) REVERT: C 118 GLU cc_start: 0.8115 (mt-10) cc_final: 0.6985 (mm-30) REVERT: C 199 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7463 (mt-10) REVERT: D 38 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: D 51 LYS cc_start: 0.8220 (mttt) cc_final: 0.7532 (mtmm) REVERT: D 154 ARG cc_start: 0.7532 (tpt90) cc_final: 0.6959 (tpt90) REVERT: D 189 PHE cc_start: 0.8044 (m-10) cc_final: 0.7667 (m-10) REVERT: E 8 TYR cc_start: 0.7768 (m-10) cc_final: 0.7294 (m-10) REVERT: E 66 TYR cc_start: 0.9010 (m-80) cc_final: 0.8708 (m-80) REVERT: E 266 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8528 (tt) outliers start: 45 outliers final: 32 residues processed: 236 average time/residue: 0.2690 time to fit residues: 95.6152 Evaluate side-chains 228 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 769 PHE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 14 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.0570 chunk 165 optimal weight: 0.0000 chunk 152 optimal weight: 0.0270 chunk 87 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.146322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107712 restraints weight = 20776.978| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.59 r_work: 0.3146 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14570 Z= 0.132 Angle : 0.525 15.306 19739 Z= 0.260 Chirality : 0.040 0.174 2312 Planarity : 0.004 0.070 2488 Dihedral : 7.315 80.511 2009 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.28 % Rotamer: Outliers : 2.68 % Allowed : 19.10 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1762 helix: 1.65 (0.16), residues: 1013 sheet: -0.58 (0.40), residues: 150 loop : -0.03 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 266 HIS 0.003 0.001 HIS B 44 PHE 0.023 0.001 PHE A 722 TYR 0.017 0.001 TYR C 71 ARG 0.005 0.000 ARG C 207 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 731) hydrogen bonds : angle 4.03447 ( 2154) covalent geometry : bond 0.00313 (14570) covalent geometry : angle 0.52540 (19739) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.7268 (m-80) cc_final: 0.7004 (m-80) REVERT: A 361 TYR cc_start: 0.8328 (p90) cc_final: 0.7976 (p90) REVERT: A 406 ASN cc_start: 0.9049 (t0) cc_final: 0.8451 (m110) REVERT: A 549 ASN cc_start: 0.9370 (t0) cc_final: 0.9143 (t0) REVERT: A 588 MET cc_start: 0.7579 (mtt) cc_final: 0.7044 (mtp) REVERT: A 769 PHE cc_start: 0.4448 (OUTLIER) cc_final: 0.4096 (m-80) REVERT: B 255 ASP cc_start: 0.8995 (m-30) cc_final: 0.8658 (m-30) REVERT: C 34 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7353 (pt) REVERT: C 118 GLU cc_start: 0.8099 (mt-10) cc_final: 0.6958 (mm-30) REVERT: D 38 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: D 51 LYS cc_start: 0.8230 (mttt) cc_final: 0.7540 (mtmm) REVERT: D 154 ARG cc_start: 0.7539 (tpt90) cc_final: 0.6975 (tpt90) REVERT: D 189 PHE cc_start: 0.7971 (m-10) cc_final: 0.7706 (m-10) REVERT: E 8 TYR cc_start: 0.7770 (m-10) cc_final: 0.7299 (m-10) REVERT: E 266 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8529 (tt) outliers start: 43 outliers final: 33 residues processed: 231 average time/residue: 0.2419 time to fit residues: 83.3949 Evaluate side-chains 228 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 769 PHE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 chunk 3 optimal weight: 0.0970 chunk 101 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN E 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108608 restraints weight = 20883.358| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.57 r_work: 0.3158 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14570 Z= 0.117 Angle : 0.510 15.237 19739 Z= 0.253 Chirality : 0.040 0.162 2312 Planarity : 0.004 0.070 2488 Dihedral : 7.256 79.790 2009 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 2.36 % Allowed : 19.48 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1762 helix: 1.70 (0.17), residues: 1014 sheet: -0.59 (0.40), residues: 150 loop : -0.01 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP A 266 HIS 0.003 0.001 HIS B 44 PHE 0.019 0.001 PHE A 722 TYR 0.016 0.001 TYR A 361 ARG 0.004 0.000 ARG C 207 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 731) hydrogen bonds : angle 3.98547 ( 2154) covalent geometry : bond 0.00274 (14570) covalent geometry : angle 0.51003 (19739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6666.06 seconds wall clock time: 116 minutes 46.20 seconds (7006.20 seconds total)