Starting phenix.real_space_refine on Thu Jul 31 07:41:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cdd_16569/07_2025/8cdd_16569.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cdd_16569/07_2025/8cdd_16569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cdd_16569/07_2025/8cdd_16569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cdd_16569/07_2025/8cdd_16569.map" model { file = "/net/cci-nas-00/data/ceres_data/8cdd_16569/07_2025/8cdd_16569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cdd_16569/07_2025/8cdd_16569.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.013 sd= 1.197 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 8327 2.51 5 N 2185 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13139 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4793 Classifications: {'peptide': 590} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 576} Chain breaks: 2 Chain: "B" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2710 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 6, 'TRANS': 319} Chain: "C" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2516 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 3, 'TRANS': 292} Chain breaks: 1 Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 195} Chain: "E" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1568 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Time building chain proxies: 8.84, per 1000 atoms: 0.67 Number of scatterers: 13139 At special positions: 0 Unit cell: (88.192, 158.08, 168.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2535 8.00 N 2185 7.00 C 8327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 140 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 244 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 461 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 443 " distance=2.03 Simple disulfide: pdb=" SG CYS A 576 " - pdb=" SG CYS A 637 " distance=2.03 Simple disulfide: pdb=" SG CYS A 594 " - pdb=" SG CYS A 625 " distance=2.03 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A 650 " distance=2.04 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 659 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 674 " distance=2.02 Simple disulfide: pdb=" SG CYS A 680 " - pdb=" SG CYS A 691 " distance=2.03 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS A 701 " distance=2.03 Simple disulfide: pdb=" SG CYS A 703 " - pdb=" SG CYS A 714 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 64 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 268 " distance=2.03 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 327 " distance=2.04 Simple disulfide: pdb=" SG CYS C 224 " - pdb=" SG CYS C 317 " distance=2.04 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 351 " distance=2.04 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 115 " distance=2.03 Simple disulfide: pdb=" SG CYS E 123 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 228 " distance=2.03 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: 3.13 Conformation dependent library (CDL) restraints added in 1.6 seconds 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3092 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 29 sheets defined 23.1% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.746A pdb=" N LYS A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.510A pdb=" N THR A 327 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 393 through 396 Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 600 through 608 Processing helix chain 'A' and resid 614 through 619 removed outlier: 3.503A pdb=" N ILE A 618 " --> pdb=" O ASP A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.798A pdb=" N SER A 682 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 194 Processing helix chain 'C' and resid 195 through 201 removed outlier: 6.986A pdb=" N SER C 198 " --> pdb=" O HIS C 195 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY C 201 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 222 Processing helix chain 'C' and resid 224 through 240 removed outlier: 3.889A pdb=" N LYS C 228 " --> pdb=" O CYS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 341 removed outlier: 5.959A pdb=" N ASN C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP C 324 " --> pdb=" O ASN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 364 Processing helix chain 'C' and resid 364 through 374 Processing helix chain 'C' and resid 375 through 402 removed outlier: 3.501A pdb=" N ASP C 379 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 392 " --> pdb=" O GLN C 388 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 399 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 400 " --> pdb=" O ASN C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 442 removed outlier: 4.409A pdb=" N ASP C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR C 409 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 445 No H-bonds generated for 'chain 'C' and resid 443 through 445' Processing helix chain 'C' and resid 451 through 506 removed outlier: 3.629A pdb=" N ASN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 486 " --> pdb=" O THR C 482 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN C 506 " --> pdb=" O GLN C 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.517A pdb=" N ASP D 100 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU D 101 " --> pdb=" O ALA D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 139 through 143 removed outlier: 4.148A pdb=" N LEU D 143 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 removed outlier: 3.931A pdb=" N GLU D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 removed outlier: 3.612A pdb=" N TYR E 52 " --> pdb=" O PHE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 removed outlier: 3.971A pdb=" N THR E 110 " --> pdb=" O ALA E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 190 No H-bonds generated for 'chain 'E' and resid 188 through 190' Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 74 removed outlier: 3.557A pdb=" N TYR A 68 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 150 " --> pdb=" O TYR A 70 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE A 72 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE A 148 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 169 removed outlier: 5.962A pdb=" N GLN A 243 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU A 187 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 245 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE A 185 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B 285 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE B 291 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL B 283 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER B 293 " --> pdb=" O GLN B 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 273 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 339 Processing sheet with id=AA7, first strand: chain 'A' and resid 387 through 391 removed outlier: 6.217A pdb=" N LEU A 473 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL A 409 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL A 475 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE A 407 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 391 removed outlier: 6.127A pdb=" N CYS A 474 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE A 381 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N ILE A 560 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N CYS A 637 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR A 630 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU A 588 " --> pdb=" O TYR A 630 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE A 632 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 586 " --> pdb=" O PHE A 632 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER A 634 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER A 638 " --> pdb=" O LYS A 580 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 398 through 400 Processing sheet with id=AB1, first strand: chain 'A' and resid 649 through 652 Processing sheet with id=AB2, first strand: chain 'A' and resid 689 through 694 removed outlier: 3.516A pdb=" N LYS A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 710 removed outlier: 3.730A pdb=" N LYS A 708 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 715 " --> pdb=" O LYS A 708 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.631A pdb=" N TRP B 87 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS B 43 " --> pdb=" O TRP B 87 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR B 89 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 60 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.483A pdb=" N ARG B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AB7, first strand: chain 'B' and resid 147 through 151 removed outlier: 3.723A pdb=" N GLU B 113 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.563A pdb=" N PHE B 177 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE B 196 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 214 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS B 198 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 237 " --> pdb=" O CYS B 258 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 233 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR B 242 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE B 227 " --> pdb=" O TYR B 242 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.610A pdb=" N ILE D 66 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN D 54 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR D 64 " --> pdb=" O GLN D 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 29 through 32 Processing sheet with id=AC3, first strand: chain 'D' and resid 38 through 43 Processing sheet with id=AC4, first strand: chain 'D' and resid 132 through 136 removed outlier: 4.489A pdb=" N SER D 149 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU D 199 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL D 151 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU D 197 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU D 153 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N SER D 195 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASN D 155 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU D 193 " --> pdb=" O ASN D 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 171 through 172 removed outlier: 3.841A pdb=" N CYS D 212 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS D 225 " --> pdb=" O CYS D 212 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 214 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL D 223 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 22 through 26 removed outlier: 3.679A pdb=" N ARG E 99 " --> pdb=" O SER E 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 30 through 31 removed outlier: 7.348A pdb=" N MET E 54 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER E 70 " --> pdb=" O MET E 54 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TRP E 56 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 30 through 31 removed outlier: 6.456A pdb=" N CYS E 115 " --> pdb=" O TRP E 135 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TRP E 135 " --> pdb=" O CYS E 115 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYS E 117 " --> pdb=" O ASP E 133 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 168 through 177 removed outlier: 3.665A pdb=" N SER E 212 " --> pdb=" O CYS E 172 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL E 174 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU E 210 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TYR E 208 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 168 through 177 removed outlier: 3.665A pdb=" N SER E 212 " --> pdb=" O CYS E 172 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL E 174 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU E 210 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TYR E 208 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 183 through 186 removed outlier: 3.842A pdb=" N CYS E 228 " --> pdb=" O LYS E 241 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS E 241 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL E 230 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL E 239 " --> pdb=" O VAL E 230 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1404 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: 4.23 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4213 1.34 - 1.46: 3222 1.46 - 1.58: 5871 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 13418 Sorted by residual: bond pdb=" N ASP B 263 " pdb=" CA ASP B 263 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.14e+00 bond pdb=" CB GLU C 362 " pdb=" CG GLU C 362 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.52e+00 bond pdb=" CB LYS C 366 " pdb=" CG LYS C 366 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" CB LYS A 708 " pdb=" CG LYS A 708 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.72e+00 bond pdb=" CA GLN A 577 " pdb=" CB GLN A 577 " ideal model delta sigma weight residual 1.524 1.540 -0.015 1.22e-02 6.72e+03 1.55e+00 ... (remaining 13413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 17910 2.59 - 5.18: 170 5.18 - 7.76: 25 7.76 - 10.35: 9 10.35 - 12.94: 2 Bond angle restraints: 18116 Sorted by residual: angle pdb=" CA GLN E 95 " pdb=" CB GLN E 95 " pdb=" CG GLN E 95 " ideal model delta sigma weight residual 114.10 123.10 -9.00 2.00e+00 2.50e-01 2.02e+01 angle pdb=" CB MET A 91 " pdb=" CG MET A 91 " pdb=" SD MET A 91 " ideal model delta sigma weight residual 112.70 125.64 -12.94 3.00e+00 1.11e-01 1.86e+01 angle pdb=" CB MET C 330 " pdb=" CG MET C 330 " pdb=" SD MET C 330 " ideal model delta sigma weight residual 112.70 123.94 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA ILE C 368 " pdb=" CB ILE C 368 " pdb=" CG1 ILE C 368 " ideal model delta sigma weight residual 110.40 116.66 -6.26 1.70e+00 3.46e-01 1.36e+01 angle pdb=" CA GLU C 362 " pdb=" CB GLU C 362 " pdb=" CG GLU C 362 " ideal model delta sigma weight residual 114.10 121.28 -7.18 2.00e+00 2.50e-01 1.29e+01 ... (remaining 18111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6864 17.81 - 35.62: 942 35.62 - 53.43: 277 53.43 - 71.24: 51 71.24 - 89.05: 19 Dihedral angle restraints: 8153 sinusoidal: 3332 harmonic: 4821 Sorted by residual: dihedral pdb=" CB CYS C 224 " pdb=" SG CYS C 224 " pdb=" SG CYS C 317 " pdb=" CB CYS C 317 " ideal model delta sinusoidal sigma weight residual 93.00 165.29 -72.29 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CB CYS A 641 " pdb=" SG CYS A 641 " pdb=" SG CYS A 650 " pdb=" CB CYS A 650 " ideal model delta sinusoidal sigma weight residual 93.00 164.12 -71.12 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS D 152 " pdb=" SG CYS D 152 " pdb=" SG CYS D 212 " pdb=" CB CYS D 212 " ideal model delta sinusoidal sigma weight residual 93.00 160.37 -67.37 1 1.00e+01 1.00e-02 5.91e+01 ... (remaining 8150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1606 0.052 - 0.105: 296 0.105 - 0.157: 66 0.157 - 0.209: 2 0.209 - 0.261: 2 Chirality restraints: 1972 Sorted by residual: chirality pdb=" CG LEU C 343 " pdb=" CB LEU C 343 " pdb=" CD1 LEU C 343 " pdb=" CD2 LEU C 343 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CG LEU A 694 " pdb=" CB LEU A 694 " pdb=" CD1 LEU A 694 " pdb=" CD2 LEU A 694 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE C 368 " pdb=" CA ILE C 368 " pdb=" CG1 ILE C 368 " pdb=" CG2 ILE C 368 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 1969 not shown) Planarity restraints: 2322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 694 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO A 695 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 695 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 695 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 663 " 0.032 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 664 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 664 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 664 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 287 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C ASN B 287 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN B 287 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 288 " 0.010 2.00e-02 2.50e+03 ... (remaining 2319 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 680 2.71 - 3.26: 13346 3.26 - 3.81: 21913 3.81 - 4.35: 26445 4.35 - 4.90: 45117 Nonbonded interactions: 107501 Sorted by model distance: nonbonded pdb=" OH TYR D 53 " pdb=" O VAL E 129 " model vdw 2.169 3.040 nonbonded pdb=" OH TYR C 194 " pdb=" OH TYR C 363 " model vdw 2.186 3.040 nonbonded pdb=" O PHE A 621 " pdb=" NE2 GLN A 629 " model vdw 2.198 3.120 nonbonded pdb=" O ILE C 431 " pdb=" OG1 THR C 435 " model vdw 2.199 3.040 nonbonded pdb=" N GLN C 342 " pdb=" OE1 GLN C 342 " model vdw 2.202 3.120 ... (remaining 107496 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=0.00 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: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.010 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 0.048 13453 Z= 0.142 Angle : 0.661 12.939 18186 Z= 0.340 Chirality : 0.044 0.261 1972 Planarity : 0.003 0.053 2322 Dihedral : 17.783 89.051 4956 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.61 % Allowed : 33.67 % Favored : 62.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -0.95 (0.21), residues: 1615 helix: 1.03 (0.31), residues: 306 sheet: -0.32 (0.24), residues: 516 loop : -1.52 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 447 HIS 0.004 0.001 HIS C 359 PHE 0.021 0.001 PHE C 350 TYR 0.016 0.001 TYR C 185 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.20789 ( 503) hydrogen bonds : angle 8.02984 ( 1404) SS BOND : bond 0.00294 ( 35) SS BOND : angle 1.19068 ( 70) covalent geometry : bond 0.00310 (13418) covalent geometry : angle 0.65833 (18116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 109 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 LYS cc_start: 0.8699 (mppt) cc_final: 0.8368 (mmpt) outliers start: 54 outliers final: 49 residues processed: 158 average time/residue: 0.9545 time to fit residues: 169.1807 Evaluate side-chains 155 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 106 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 148 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 HIS A 388 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 311 ASN C 159 ASN C 352 ASN C 414 HIS D 68 ASN D 142 GLN E 59 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.093236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.070156 restraints weight = 41281.271| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 4.01 r_work: 0.3312 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13453 Z= 0.154 Angle : 0.618 8.536 18186 Z= 0.326 Chirality : 0.044 0.164 1972 Planarity : 0.004 0.061 2322 Dihedral : 7.426 58.537 1849 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 6.48 % Allowed : 28.52 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -0.90 (0.21), residues: 1615 helix: 1.22 (0.30), residues: 309 sheet: -0.29 (0.23), residues: 501 loop : -1.55 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 87 HIS 0.006 0.001 HIS C 474 PHE 0.016 0.001 PHE A 468 TYR 0.014 0.001 TYR C 185 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 503) hydrogen bonds : angle 5.98133 ( 1404) SS BOND : bond 0.00328 ( 35) SS BOND : angle 0.90652 ( 70) covalent geometry : bond 0.00334 (13418) covalent geometry : angle 0.61661 (18116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 124 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8737 (t0) REVERT: A 254 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7484 (pm20) REVERT: A 635 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.7383 (p90) REVERT: B 38 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: B 339 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7513 (ttp80) REVERT: B 344 TYR cc_start: 0.8683 (p90) cc_final: 0.8478 (p90) REVERT: C 194 TYR cc_start: 0.8547 (m-80) cc_final: 0.8158 (m-80) REVERT: C 425 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8668 (tp30) REVERT: C 513 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5111 (pp20) REVERT: D 160 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7547 (ppp80) REVERT: E 108 GLU cc_start: 0.8516 (pm20) cc_final: 0.8167 (pm20) REVERT: E 142 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8157 (tp) REVERT: E 177 TYR cc_start: 0.7718 (p90) cc_final: 0.7233 (p90) outliers start: 97 outliers final: 35 residues processed: 207 average time/residue: 0.8935 time to fit residues: 207.9016 Evaluate side-chains 154 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 182 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 388 GLN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN C 159 ASN C 389 GLN C 477 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.091120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.067790 restraints weight = 42270.888| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.01 r_work: 0.3249 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13453 Z= 0.239 Angle : 0.654 8.664 18186 Z= 0.346 Chirality : 0.046 0.257 1972 Planarity : 0.004 0.071 2322 Dihedral : 6.603 56.659 1806 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 6.61 % Allowed : 28.32 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -1.02 (0.21), residues: 1615 helix: 1.16 (0.30), residues: 310 sheet: -0.44 (0.23), residues: 512 loop : -1.59 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 87 HIS 0.006 0.001 HIS C 474 PHE 0.021 0.002 PHE A 468 TYR 0.018 0.002 TYR A 413 ARG 0.005 0.000 ARG C 448 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 503) hydrogen bonds : angle 5.81961 ( 1404) SS BOND : bond 0.00664 ( 35) SS BOND : angle 0.90775 ( 70) covalent geometry : bond 0.00534 (13418) covalent geometry : angle 0.65294 (18116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 115 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 PHE cc_start: 0.8948 (m-10) cc_final: 0.8538 (m-10) REVERT: A 423 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.7872 (tt) REVERT: A 471 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: A 635 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.7552 (p90) REVERT: B 38 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: B 174 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8267 (ptm160) REVERT: C 184 TYR cc_start: 0.8110 (t80) cc_final: 0.7505 (t80) REVERT: C 194 TYR cc_start: 0.8900 (m-80) cc_final: 0.8184 (m-80) REVERT: C 425 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8723 (tp30) REVERT: E 108 GLU cc_start: 0.8493 (pm20) cc_final: 0.8096 (pm20) REVERT: E 142 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8166 (tp) REVERT: E 177 TYR cc_start: 0.7895 (p90) cc_final: 0.6882 (p90) outliers start: 99 outliers final: 46 residues processed: 205 average time/residue: 0.9123 time to fit residues: 211.3582 Evaluate side-chains 159 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 106 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 182 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 127 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 388 GLN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN E 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.092837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.069765 restraints weight = 41424.504| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.99 r_work: 0.3300 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13453 Z= 0.139 Angle : 0.617 10.403 18186 Z= 0.322 Chirality : 0.044 0.174 1972 Planarity : 0.004 0.060 2322 Dihedral : 6.306 55.806 1796 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 6.48 % Allowed : 29.06 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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 (0.21), residues: 1615 helix: 1.30 (0.30), residues: 308 sheet: -0.51 (0.23), residues: 503 loop : -1.50 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 52 HIS 0.005 0.001 HIS E 232 PHE 0.018 0.001 PHE D 134 TYR 0.014 0.001 TYR C 185 ARG 0.005 0.000 ARG C 458 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 503) hydrogen bonds : angle 5.51862 ( 1404) SS BOND : bond 0.00340 ( 35) SS BOND : angle 1.34891 ( 70) covalent geometry : bond 0.00311 (13418) covalent geometry : angle 0.61296 (18116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 118 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 PHE cc_start: 0.8904 (m-10) cc_final: 0.8564 (m-10) REVERT: A 423 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7812 (tt) REVERT: A 424 ASN cc_start: 0.7147 (OUTLIER) cc_final: 0.6942 (t0) REVERT: A 562 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8460 (mtpp) REVERT: A 635 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.7483 (p90) REVERT: B 38 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: B 148 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8512 (tp30) REVERT: B 174 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8211 (ptm160) REVERT: B 339 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7557 (ttp80) REVERT: C 184 TYR cc_start: 0.7976 (t80) cc_final: 0.7434 (t80) REVERT: C 194 TYR cc_start: 0.8938 (m-80) cc_final: 0.8038 (m-80) REVERT: C 425 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8570 (tp30) REVERT: C 460 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8027 (mm) REVERT: D 125 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8150 (mm) REVERT: D 228 ASN cc_start: 0.8363 (p0) cc_final: 0.8125 (t0) REVERT: E 108 GLU cc_start: 0.8519 (pm20) cc_final: 0.8138 (pm20) REVERT: E 142 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8152 (tp) REVERT: E 177 TYR cc_start: 0.7842 (p90) cc_final: 0.6874 (p90) outliers start: 97 outliers final: 38 residues processed: 202 average time/residue: 0.9480 time to fit residues: 215.0619 Evaluate side-chains 147 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 97 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 182 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 61 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 388 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.092329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.069121 restraints weight = 41902.103| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.99 r_work: 0.3286 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13453 Z= 0.172 Angle : 0.635 9.274 18186 Z= 0.334 Chirality : 0.046 0.323 1972 Planarity : 0.004 0.061 2322 Dihedral : 6.309 59.145 1792 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.54 % Allowed : 30.39 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -0.93 (0.21), residues: 1615 helix: 1.36 (0.30), residues: 304 sheet: -0.50 (0.23), residues: 504 loop : -1.48 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 447 HIS 0.007 0.001 HIS B 104 PHE 0.016 0.001 PHE A 468 TYR 0.016 0.001 TYR C 185 ARG 0.005 0.001 ARG B 229 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 503) hydrogen bonds : angle 5.44832 ( 1404) SS BOND : bond 0.00348 ( 35) SS BOND : angle 0.97326 ( 70) covalent geometry : bond 0.00388 (13418) covalent geometry : angle 0.63381 (18116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 108 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 PHE cc_start: 0.8956 (m-10) cc_final: 0.8738 (m-10) REVERT: A 423 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.7801 (tt) REVERT: A 562 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8549 (mtpp) REVERT: A 635 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7587 (p90) REVERT: B 38 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: B 148 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8501 (tp30) REVERT: B 174 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8263 (ptm160) REVERT: C 184 TYR cc_start: 0.8022 (t80) cc_final: 0.7508 (t80) REVERT: C 220 VAL cc_start: 0.9426 (t) cc_final: 0.9210 (p) REVERT: C 425 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8651 (tp30) REVERT: C 460 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8025 (mm) REVERT: E 108 GLU cc_start: 0.8525 (pm20) cc_final: 0.8163 (pm20) REVERT: E 142 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8207 (tp) REVERT: E 177 TYR cc_start: 0.7880 (p90) cc_final: 0.7013 (p90) outliers start: 83 outliers final: 48 residues processed: 183 average time/residue: 1.2283 time to fit residues: 251.4896 Evaluate side-chains 155 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 98 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 182 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 106 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN E 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.093286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.070231 restraints weight = 42244.172| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 4.04 r_work: 0.3243 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13453 Z= 0.223 Angle : 0.656 10.140 18186 Z= 0.348 Chirality : 0.046 0.184 1972 Planarity : 0.004 0.059 2322 Dihedral : 6.358 58.678 1791 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 6.01 % Allowed : 30.19 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -1.02 (0.21), residues: 1615 helix: 1.40 (0.30), residues: 297 sheet: -0.65 (0.23), residues: 513 loop : -1.49 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 447 HIS 0.004 0.001 HIS B 104 PHE 0.019 0.002 PHE D 134 TYR 0.017 0.002 TYR A 413 ARG 0.004 0.001 ARG C 448 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 503) hydrogen bonds : angle 5.48624 ( 1404) SS BOND : bond 0.00430 ( 35) SS BOND : angle 0.93329 ( 70) covalent geometry : bond 0.00500 (13418) covalent geometry : angle 0.65465 (18116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 105 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 PHE cc_start: 0.9025 (m-10) cc_final: 0.8721 (m-10) REVERT: A 423 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.7904 (tt) REVERT: A 562 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8620 (mtpp) REVERT: A 635 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.7691 (p90) REVERT: B 38 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: B 174 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8320 (ptm160) REVERT: C 184 TYR cc_start: 0.7875 (t80) cc_final: 0.7392 (t80) REVERT: C 220 VAL cc_start: 0.9459 (t) cc_final: 0.9243 (p) REVERT: C 425 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8624 (tp30) REVERT: C 460 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8000 (mm) REVERT: E 108 GLU cc_start: 0.8575 (pm20) cc_final: 0.8190 (pm20) REVERT: E 142 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8175 (tp) REVERT: E 177 TYR cc_start: 0.7986 (p90) cc_final: 0.7128 (p90) REVERT: E 227 ILE cc_start: 0.8932 (tp) cc_final: 0.8523 (pp) outliers start: 90 outliers final: 51 residues processed: 188 average time/residue: 0.9262 time to fit residues: 197.7582 Evaluate side-chains 155 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 96 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 182 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 116 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 0.0170 chunk 79 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 388 GLN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 229 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.095489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.072455 restraints weight = 41872.749| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 4.09 r_work: 0.3294 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.003 0.043 13453 Z= 0.134 Angle : 0.635 10.821 18186 Z= 0.334 Chirality : 0.045 0.175 1972 Planarity : 0.004 0.058 2322 Dihedral : 5.893 57.114 1788 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.14 % Allowed : 31.33 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -0.89 (0.21), residues: 1615 helix: 1.45 (0.30), residues: 296 sheet: -0.56 (0.23), residues: 499 loop : -1.37 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 447 HIS 0.004 0.001 HIS E 232 PHE 0.019 0.001 PHE C 350 TYR 0.017 0.001 TYR C 185 ARG 0.005 0.000 ARG B 229 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 503) hydrogen bonds : angle 5.29279 ( 1404) SS BOND : bond 0.00264 ( 35) SS BOND : angle 0.77423 ( 70) covalent geometry : bond 0.00303 (13418) covalent geometry : angle 0.63455 (18116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 110 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 PHE cc_start: 0.8995 (m-10) cc_final: 0.8711 (m-10) REVERT: A 423 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7837 (tt) REVERT: B 38 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: B 148 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8631 (tp30) REVERT: B 174 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8240 (ptm160) REVERT: B 339 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7507 (ttm110) REVERT: C 184 TYR cc_start: 0.7906 (t80) cc_final: 0.7467 (t80) REVERT: C 194 TYR cc_start: 0.8615 (m-80) cc_final: 0.7805 (m-80) REVERT: C 425 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8702 (tp30) REVERT: E 66 GLU cc_start: 0.7752 (tt0) cc_final: 0.7541 (mt-10) REVERT: E 95 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7611 (pp30) REVERT: E 97 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8307 (m) REVERT: E 108 GLU cc_start: 0.8594 (pm20) cc_final: 0.8199 (pm20) REVERT: E 142 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8194 (tp) REVERT: E 177 TYR cc_start: 0.7880 (p90) cc_final: 0.7077 (p90) REVERT: E 227 ILE cc_start: 0.8938 (tp) cc_final: 0.8536 (pp) outliers start: 77 outliers final: 43 residues processed: 175 average time/residue: 0.9107 time to fit residues: 179.6502 Evaluate side-chains 156 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 104 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 80 optimal weight: 0.0020 chunk 6 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 136 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 229 ASN E 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.095867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.072931 restraints weight = 41904.086| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 4.05 r_work: 0.3307 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13453 Z= 0.132 Angle : 0.649 11.535 18186 Z= 0.336 Chirality : 0.046 0.462 1972 Planarity : 0.004 0.054 2322 Dihedral : 5.714 57.166 1784 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.21 % Allowed : 32.26 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -0.83 (0.21), residues: 1615 helix: 1.47 (0.30), residues: 296 sheet: -0.50 (0.24), residues: 499 loop : -1.33 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 447 HIS 0.006 0.001 HIS B 104 PHE 0.020 0.001 PHE D 134 TYR 0.016 0.001 TYR C 185 ARG 0.006 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 503) hydrogen bonds : angle 5.19381 ( 1404) SS BOND : bond 0.00250 ( 35) SS BOND : angle 0.74098 ( 70) covalent geometry : bond 0.00299 (13418) covalent geometry : angle 0.64907 (18116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 117 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 PHE cc_start: 0.8992 (m-10) cc_final: 0.8721 (m-10) REVERT: A 385 ASN cc_start: 0.8642 (t0) cc_final: 0.8259 (t0) REVERT: A 423 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.7854 (tt) REVERT: B 38 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: B 174 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8225 (ptm160) REVERT: B 339 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7489 (ttm110) REVERT: C 184 TYR cc_start: 0.7847 (t80) cc_final: 0.7483 (t80) REVERT: C 194 TYR cc_start: 0.8706 (m-80) cc_final: 0.8249 (m-80) REVERT: C 425 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8615 (tp30) REVERT: E 66 GLU cc_start: 0.7655 (tt0) cc_final: 0.7402 (mt-10) REVERT: E 108 GLU cc_start: 0.8599 (pm20) cc_final: 0.8198 (pm20) REVERT: E 142 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8201 (tp) REVERT: E 177 TYR cc_start: 0.7844 (p90) cc_final: 0.7054 (p90) REVERT: E 227 ILE cc_start: 0.8957 (tp) cc_final: 0.8564 (pp) outliers start: 63 outliers final: 44 residues processed: 169 average time/residue: 1.1295 time to fit residues: 214.0826 Evaluate side-chains 154 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 105 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 111 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN A 388 GLN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 229 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.095821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.072873 restraints weight = 41509.778| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 4.04 r_work: 0.3303 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13453 Z= 0.143 Angle : 0.665 12.210 18186 Z= 0.346 Chirality : 0.046 0.392 1972 Planarity : 0.004 0.058 2322 Dihedral : 5.713 57.180 1783 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.14 % Allowed : 32.06 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1615 helix: 1.49 (0.30), residues: 295 sheet: -0.50 (0.24), residues: 500 loop : -1.32 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 447 HIS 0.007 0.001 HIS B 104 PHE 0.026 0.001 PHE C 350 TYR 0.016 0.001 TYR C 185 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 503) hydrogen bonds : angle 5.18891 ( 1404) SS BOND : bond 0.00264 ( 35) SS BOND : angle 1.39216 ( 70) covalent geometry : bond 0.00327 (13418) covalent geometry : angle 0.66057 (18116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 111 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 PHE cc_start: 0.8958 (m-10) cc_final: 0.8686 (m-10) REVERT: A 423 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.7900 (tt) REVERT: B 38 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: B 174 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8314 (ptm160) REVERT: B 339 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7613 (ttm110) REVERT: C 184 TYR cc_start: 0.7884 (t80) cc_final: 0.7642 (t80) REVERT: C 194 TYR cc_start: 0.8668 (m-80) cc_final: 0.7682 (m-80) REVERT: C 425 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8657 (tp30) REVERT: E 66 GLU cc_start: 0.7706 (tt0) cc_final: 0.7451 (mt-10) REVERT: E 98 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7559 (tp) REVERT: E 108 GLU cc_start: 0.8597 (pm20) cc_final: 0.8211 (pm20) REVERT: E 142 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8247 (tp) REVERT: E 177 TYR cc_start: 0.7820 (p90) cc_final: 0.7047 (p90) REVERT: E 227 ILE cc_start: 0.8956 (tp) cc_final: 0.8558 (pp) outliers start: 62 outliers final: 46 residues processed: 159 average time/residue: 0.9968 time to fit residues: 178.1032 Evaluate side-chains 160 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 107 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 388 GLN Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 229 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 121 ASN E 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.095628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.072538 restraints weight = 41515.294| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 4.12 r_work: 0.3291 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13453 Z= 0.151 Angle : 0.677 12.649 18186 Z= 0.351 Chirality : 0.046 0.371 1972 Planarity : 0.004 0.059 2322 Dihedral : 5.708 57.397 1782 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.94 % Allowed : 32.40 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -0.80 (0.21), residues: 1615 helix: 1.46 (0.30), residues: 295 sheet: -0.47 (0.23), residues: 505 loop : -1.31 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 447 HIS 0.021 0.001 HIS B 104 PHE 0.020 0.001 PHE A 219 TYR 0.018 0.001 TYR C 185 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 503) hydrogen bonds : angle 5.18405 ( 1404) SS BOND : bond 0.00278 ( 35) SS BOND : angle 1.29747 ( 70) covalent geometry : bond 0.00346 (13418) covalent geometry : angle 0.67315 (18116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 111 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 PHE cc_start: 0.8972 (m-10) cc_final: 0.8701 (m-10) REVERT: A 423 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.7925 (tt) REVERT: B 38 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: B 174 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8339 (ptm160) REVERT: B 339 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7661 (ttm110) REVERT: C 184 TYR cc_start: 0.7906 (t80) cc_final: 0.7614 (t80) REVERT: C 194 TYR cc_start: 0.8658 (m-80) cc_final: 0.8339 (m-80) REVERT: C 425 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8667 (tp30) REVERT: E 47 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8188 (m-10) REVERT: E 66 GLU cc_start: 0.7773 (tt0) cc_final: 0.7525 (mt-10) REVERT: E 98 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7548 (tp) REVERT: E 108 GLU cc_start: 0.8603 (pm20) cc_final: 0.8221 (pm20) REVERT: E 142 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8214 (tp) REVERT: E 177 TYR cc_start: 0.7819 (p90) cc_final: 0.7074 (p90) REVERT: E 227 ILE cc_start: 0.8886 (tp) cc_final: 0.8458 (pp) outliers start: 59 outliers final: 45 residues processed: 159 average time/residue: 1.0146 time to fit residues: 182.0889 Evaluate side-chains 160 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 108 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN A 477 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 229 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.094485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.071367 restraints weight = 41695.577| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 4.03 r_work: 0.3267 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13453 Z= 0.191 Angle : 0.691 12.689 18186 Z= 0.361 Chirality : 0.047 0.347 1972 Planarity : 0.004 0.059 2322 Dihedral : 5.823 58.448 1782 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.01 % Allowed : 32.53 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -0.88 (0.21), residues: 1615 helix: 1.37 (0.30), residues: 296 sheet: -0.52 (0.23), residues: 504 loop : -1.36 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 87 HIS 0.022 0.001 HIS B 104 PHE 0.026 0.002 PHE C 350 TYR 0.018 0.001 TYR C 190 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 503) hydrogen bonds : angle 5.28510 ( 1404) SS BOND : bond 0.00375 ( 35) SS BOND : angle 1.26341 ( 70) covalent geometry : bond 0.00435 (13418) covalent geometry : angle 0.68831 (18116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12276.54 seconds wall clock time: 216 minutes 42.95 seconds (13002.95 seconds total)