Starting phenix.real_space_refine on Thu Jun 19 02:37:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z40_39759/06_2025/8z40_39759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z40_39759/06_2025/8z40_39759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z40_39759/06_2025/8z40_39759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z40_39759/06_2025/8z40_39759.map" model { file = "/net/cci-nas-00/data/ceres_data/8z40_39759/06_2025/8z40_39759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z40_39759/06_2025/8z40_39759.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 100 5.16 5 C 13778 2.51 5 N 4087 2.21 5 O 3928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21893 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4802 Classifications: {'peptide': 614} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 40, 'TRANS': 573} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4807 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 40, 'TRANS': 572} Chain breaks: 1 Chain: "C" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3065 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 26, 'TRANS': 368} Chain breaks: 1 Chain: "D" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3075 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 27, 'TRANS': 368} Chain breaks: 2 Chain: "E" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3072 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 27, 'TRANS': 368} Chain breaks: 1 Chain: "F" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3072 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 27, 'TRANS': 368} Chain breaks: 1 Time building chain proxies: 14.56, per 1000 atoms: 0.67 Number of scatterers: 21893 At special positions: 0 Unit cell: (100.28, 138, 175.72, 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 100 16.00 O 3928 8.00 N 4087 7.00 C 13778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.16 Conformation dependent library (CDL) restraints added in 2.8 seconds 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5182 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 11 sheets defined 52.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.802A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.926A pdb=" N MET A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.722A pdb=" N ALA A 230 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 231 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 232 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 250 through 256 removed outlier: 3.539A pdb=" N TRP A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.570A pdb=" N LYS A 289 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 290 " --> pdb=" O PRO A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.534A pdb=" N ARG A 385 " --> pdb=" O MET A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 428 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.518A pdb=" N ARG A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 removed outlier: 3.733A pdb=" N ILE A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 570 through 575 Processing helix chain 'A' and resid 577 through 589 Processing helix chain 'A' and resid 593 through 607 Processing helix chain 'A' and resid 611 through 624 Processing helix chain 'B' and resid 16 through 23 removed outlier: 3.614A pdb=" N LEU B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.838A pdb=" N ILE B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 90 removed outlier: 3.580A pdb=" N HIS B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG B 90 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.529A pdb=" N SER B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 168 through 173 removed outlier: 4.283A pdb=" N ARG B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 215 Processing helix chain 'B' and resid 217 through 221 removed outlier: 4.227A pdb=" N MET B 220 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.660A pdb=" N THR B 231 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 250 through 258 removed outlier: 3.554A pdb=" N TRP B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 273 through 282 removed outlier: 3.943A pdb=" N LEU B 277 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.533A pdb=" N LEU B 290 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 318 removed outlier: 4.075A pdb=" N GLY B 318 " --> pdb=" O TYR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 347 Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.708A pdb=" N ARG B 385 " --> pdb=" O MET B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 428 Processing helix chain 'B' and resid 446 through 451 removed outlier: 4.236A pdb=" N ARG B 450 " --> pdb=" O ASP B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 477 through 488 removed outlier: 3.639A pdb=" N ILE B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 519 through 528 Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 570 through 575 removed outlier: 3.715A pdb=" N SER B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 589 Processing helix chain 'B' and resid 593 through 608 removed outlier: 4.093A pdb=" N LEU B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 624 Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 248 through 257 removed outlier: 3.674A pdb=" N ARG C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 274 through 282 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 310 through 317 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 328 through 347 Processing helix chain 'C' and resid 365 through 385 Processing helix chain 'C' and resid 409 through 428 removed outlier: 3.553A pdb=" N ALA C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 454 removed outlier: 3.671A pdb=" N PHE C 454 " --> pdb=" O ARG C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 465 removed outlier: 3.717A pdb=" N THR C 459 " --> pdb=" O ARG C 455 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL C 461 " --> pdb=" O GLU C 457 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 removed outlier: 3.558A pdb=" N ILE C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 513 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 554 through 561 Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 594 through 608 removed outlier: 4.049A pdb=" N LEU C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 624 Processing helix chain 'D' and resid 227 through 231 Processing helix chain 'D' and resid 232 through 241 removed outlier: 3.943A pdb=" N GLU D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 310 through 318 removed outlier: 3.869A pdb=" N GLY D 318 " --> pdb=" O TYR D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 347 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.534A pdb=" N VAL D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 428 removed outlier: 3.574A pdb=" N ALA D 413 " --> pdb=" O ASP D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 458 removed outlier: 4.060A pdb=" N ALA D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 465 removed outlier: 3.515A pdb=" N GLY D 465 " --> pdb=" O VAL D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 removed outlier: 3.524A pdb=" N ILE D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 513 Processing helix chain 'D' and resid 519 through 527 Processing helix chain 'D' and resid 530 through 534 removed outlier: 4.181A pdb=" N GLY D 533 " --> pdb=" O ARG D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 561 Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 577 through 589 Processing helix chain 'D' and resid 593 through 608 Processing helix chain 'D' and resid 611 through 625 Processing helix chain 'E' and resid 227 through 231 Processing helix chain 'E' and resid 233 through 242 Processing helix chain 'E' and resid 248 through 257 Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 286 through 290 removed outlier: 3.838A pdb=" N LYS E 289 " --> pdb=" O ASN E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 328 through 347 Processing helix chain 'E' and resid 365 through 385 Processing helix chain 'E' and resid 409 through 428 Processing helix chain 'E' and resid 457 through 465 removed outlier: 3.591A pdb=" N VAL E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG E 463 " --> pdb=" O THR E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 487 removed outlier: 3.596A pdb=" N ILE E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 513 Processing helix chain 'E' and resid 519 through 527 Processing helix chain 'E' and resid 554 through 561 Processing helix chain 'E' and resid 570 through 575 Processing helix chain 'E' and resid 577 through 589 Processing helix chain 'E' and resid 594 through 607 removed outlier: 3.748A pdb=" N LEU E 598 " --> pdb=" O ARG E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 625 Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 233 through 241 Processing helix chain 'F' and resid 248 through 258 Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 274 through 282 removed outlier: 3.655A pdb=" N ARG F 278 " --> pdb=" O GLY F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 310 through 317 removed outlier: 3.518A pdb=" N TYR F 314 " --> pdb=" O PRO F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 347 removed outlier: 3.501A pdb=" N LEU F 332 " --> pdb=" O ASP F 328 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG F 333 " --> pdb=" O PRO F 329 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU F 334 " --> pdb=" O GLY F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.556A pdb=" N ARG F 385 " --> pdb=" O MET F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 428 removed outlier: 3.591A pdb=" N ALA F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 462 removed outlier: 4.278A pdb=" N ALA F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 465 No H-bonds generated for 'chain 'F' and resid 463 through 465' Processing helix chain 'F' and resid 477 through 487 Processing helix chain 'F' and resid 502 through 513 Processing helix chain 'F' and resid 519 through 527 Processing helix chain 'F' and resid 554 through 561 Processing helix chain 'F' and resid 570 through 575 removed outlier: 3.601A pdb=" N SER F 574 " --> pdb=" O ASN F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 589 Processing helix chain 'F' and resid 593 through 607 removed outlier: 4.025A pdb=" N LEU F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU F 598 " --> pdb=" O ARG F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 624 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 62 removed outlier: 6.728A pdb=" N VAL A 32 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR A 61 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 34 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N HIS A 6 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 187 removed outlier: 5.453A pdb=" N VAL A 183 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLN A 194 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 266 removed outlier: 6.135A pdb=" N LYS A 260 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR A 350 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N HIS A 264 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ARG A 354 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N HIS A 266 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS A 395 " --> pdb=" O CYS A 349 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N VAL A 437 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU A 398 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 439 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU A 400 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL A 468 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N GLY A 494 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 470 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 8 removed outlier: 7.025A pdb=" N VAL B 32 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR B 61 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 34 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.928A pdb=" N VAL B 98 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL B 126 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 123 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 182 through 185 removed outlier: 6.473A pdb=" N ARG B 192 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 260 through 266 removed outlier: 4.908A pdb=" N ILE B 261 " --> pdb=" O TYR B 350 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLU B 352 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU B 263 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG B 354 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 265 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B 395 " --> pdb=" O CYS B 349 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL B 437 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 398 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 439 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 400 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 467 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL B 468 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N GLY B 494 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL B 470 " --> pdb=" O GLY B 494 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU B 493 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 260 through 266 removed outlier: 7.561A pdb=" N LYS C 260 " --> pdb=" O CYS C 349 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA C 351 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU C 262 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 353 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N HIS C 264 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N CYS C 355 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N HIS C 266 " --> pdb=" O CYS C 355 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS C 395 " --> pdb=" O CYS C 349 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL C 437 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU C 398 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL C 439 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU C 400 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 467 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL C 468 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N GLY C 494 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL C 470 " --> pdb=" O GLY C 494 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU C 493 " --> pdb=" O GLU C 517 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 260 through 266 removed outlier: 7.736A pdb=" N LYS D 260 " --> pdb=" O CYS D 349 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA D 351 " --> pdb=" O LYS D 260 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU D 262 " --> pdb=" O ALA D 351 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL D 353 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N HIS D 264 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N CYS D 355 " --> pdb=" O HIS D 264 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N HIS D 266 " --> pdb=" O CYS D 355 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL D 437 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU D 398 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL D 439 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 400 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL D 468 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N GLY D 494 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL D 470 " --> pdb=" O GLY D 494 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU D 493 " --> pdb=" O GLU D 517 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 260 through 266 removed outlier: 7.805A pdb=" N LYS E 260 " --> pdb=" O CYS E 349 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA E 351 " --> pdb=" O LYS E 260 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU E 262 " --> pdb=" O ALA E 351 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL E 353 " --> pdb=" O GLU E 262 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N HIS E 264 " --> pdb=" O VAL E 353 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N CYS E 355 " --> pdb=" O HIS E 264 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N HIS E 266 " --> pdb=" O CYS E 355 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL E 437 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU E 398 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL E 439 " --> pdb=" O LEU E 398 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU E 400 " --> pdb=" O VAL E 439 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA E 467 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR E 469 " --> pdb=" O VAL E 439 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL E 468 " --> pdb=" O ARG E 492 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N GLY E 494 " --> pdb=" O VAL E 468 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL E 470 " --> pdb=" O GLY E 494 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU E 493 " --> pdb=" O GLU E 517 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 260 through 266 removed outlier: 7.633A pdb=" N LYS F 260 " --> pdb=" O CYS F 349 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA F 351 " --> pdb=" O LYS F 260 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU F 262 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL F 353 " --> pdb=" O GLU F 262 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N HIS F 264 " --> pdb=" O VAL F 353 " (cutoff:3.500A) removed outlier: 10.267A pdb=" N CYS F 355 " --> pdb=" O HIS F 264 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N HIS F 266 " --> pdb=" O CYS F 355 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS F 395 " --> pdb=" O CYS F 349 " (cutoff:3.500A) removed outlier: 12.146A pdb=" N VAL F 396 " --> pdb=" O VAL F 436 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N GLY F 438 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU F 398 " --> pdb=" O GLY F 438 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASP F 440 " --> pdb=" O LEU F 398 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU F 400 " --> pdb=" O ASP F 440 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA F 467 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL F 468 " --> pdb=" O ARG F 492 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N GLY F 494 " --> pdb=" O VAL F 468 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL F 470 " --> pdb=" O GLY F 494 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU F 493 " --> pdb=" O GLU F 517 " (cutoff:3.500A) 982 hydrogen bonds defined for protein. 2850 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: 9.18 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7628 1.35 - 1.47: 4805 1.47 - 1.58: 9846 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 22401 Sorted by residual: bond pdb=" C LEU D 221 " pdb=" N PRO D 222 " ideal model delta sigma weight residual 1.335 1.360 -0.026 1.19e-02 7.06e+03 4.60e+00 bond pdb=" C ALA B 53 " pdb=" N PRO B 54 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.30e-02 5.92e+03 3.88e+00 bond pdb=" C VAL A 18 " pdb=" N PRO A 19 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.77e+00 bond pdb=" C VAL B 18 " pdb=" N PRO B 19 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.54e+00 bond pdb=" C ARG B 39 " pdb=" N PRO B 40 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.34e-02 5.57e+03 3.38e+00 ... (remaining 22396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 30084 2.50 - 5.01: 344 5.01 - 7.51: 37 7.51 - 10.01: 7 10.01 - 12.52: 4 Bond angle restraints: 30476 Sorted by residual: angle pdb=" CA LYS A 105 " pdb=" CB LYS A 105 " pdb=" CG LYS A 105 " ideal model delta sigma weight residual 114.10 126.62 -12.52 2.00e+00 2.50e-01 3.92e+01 angle pdb=" C PHE E 454 " pdb=" CA PHE E 454 " pdb=" CB PHE E 454 " ideal model delta sigma weight residual 116.63 110.83 5.80 1.16e+00 7.43e-01 2.50e+01 angle pdb=" C HIS E 452 " pdb=" CA HIS E 452 " pdb=" CB HIS E 452 " ideal model delta sigma weight residual 116.34 110.17 6.17 1.40e+00 5.10e-01 1.94e+01 angle pdb=" CA ARG A 173 " pdb=" CB ARG A 173 " pdb=" CG ARG A 173 " ideal model delta sigma weight residual 114.10 122.51 -8.41 2.00e+00 2.50e-01 1.77e+01 angle pdb=" C ASP A 532 " pdb=" CA ASP A 532 " pdb=" CB ASP A 532 " ideal model delta sigma weight residual 115.89 110.63 5.26 1.32e+00 5.74e-01 1.59e+01 ... (remaining 30471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11786 17.97 - 35.95: 1303 35.95 - 53.92: 291 53.92 - 71.89: 92 71.89 - 89.87: 14 Dihedral angle restraints: 13486 sinusoidal: 5447 harmonic: 8039 Sorted by residual: dihedral pdb=" CA ARG B 39 " pdb=" C ARG B 39 " pdb=" N PRO B 40 " pdb=" CA PRO B 40 " ideal model delta harmonic sigma weight residual -180.00 -157.00 -23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ARG C 455 " pdb=" C ARG C 455 " pdb=" N GLU C 456 " pdb=" CA GLU C 456 " ideal model delta harmonic sigma weight residual -180.00 -157.01 -22.99 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA ALA A 387 " pdb=" C ALA A 387 " pdb=" N PRO A 388 " pdb=" CA PRO A 388 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 13483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2392 0.035 - 0.070: 668 0.070 - 0.106: 229 0.106 - 0.141: 63 0.141 - 0.176: 4 Chirality restraints: 3356 Sorted by residual: chirality pdb=" CA PHE F 454 " pdb=" N PHE F 454 " pdb=" C PHE F 454 " pdb=" CB PHE F 454 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CG LEU A 100 " pdb=" CB LEU A 100 " pdb=" CD1 LEU A 100 " pdb=" CD2 LEU A 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA VAL A 34 " pdb=" N VAL A 34 " pdb=" C VAL A 34 " pdb=" CB VAL A 34 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 3353 not shown) Planarity restraints: 4049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 85 " -0.024 2.00e-02 2.50e+03 2.37e-02 1.40e+01 pdb=" CG TRP A 85 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 85 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 85 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 85 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 85 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 85 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 85 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 85 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP A 85 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 173 " -0.201 9.50e-02 1.11e+02 9.01e-02 5.46e+00 pdb=" NE ARG A 173 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 173 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 173 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 173 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP E 302 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO E 303 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 303 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 303 " 0.032 5.00e-02 4.00e+02 ... (remaining 4046 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1876 2.74 - 3.28: 21172 3.28 - 3.82: 35067 3.82 - 4.36: 39582 4.36 - 4.90: 70114 Nonbonded interactions: 167811 Sorted by model distance: nonbonded pdb=" O GLY A 167 " pdb=" NH2 ARG A 172 " model vdw 2.201 3.120 nonbonded pdb=" NH2 ARG D 354 " pdb=" OD2 ASP D 440 " model vdw 2.207 3.120 nonbonded pdb=" OE1 GLU B 186 " pdb=" NH2 ARG B 191 " model vdw 2.249 3.120 nonbonded pdb=" OH TYR B 410 " pdb=" O ARG B 450 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASN D 359 " pdb=" OG1 THR D 403 " model vdw 2.261 3.040 ... (remaining 167806 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 534 or resid 549 through 629)) selection = (chain 'B' and (resid 3 through 217 or (resid 218 and (name N or name CA or name \ C or name O )) or resid 219 through 629)) } ncs_group { reference = (chain 'C' and (resid 223 through 386 or resid 388 through 534 or resid 548 thro \ ugh 629)) selection = (chain 'D' and (resid 223 through 534 or resid 548 through 629)) selection = (chain 'E' and (resid 223 through 386 or resid 388 through 629)) selection = (chain 'F' and (resid 223 through 386 or resid 388 through 629)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.670 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: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 52.410 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.100 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:3.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 0.049 22401 Z= 0.140 Angle : 0.663 12.517 30476 Z= 0.366 Chirality : 0.039 0.176 3356 Planarity : 0.005 0.090 4049 Dihedral : 16.149 89.867 8304 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.17 % Favored : 94.61 % Rotamer: Outliers : 0.13 % Allowed : 20.86 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2784 helix: 1.86 (0.15), residues: 1291 sheet: -1.20 (0.33), residues: 245 loop : -1.59 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 85 HIS 0.005 0.001 HIS D 462 PHE 0.028 0.002 PHE D 458 TYR 0.013 0.001 TYR C 410 ARG 0.012 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.18405 ( 982) hydrogen bonds : angle 6.26609 ( 2850) covalent geometry : bond 0.00283 (22401) covalent geometry : angle 0.66294 (30476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.6954 (tptt) cc_final: 0.6740 (tptp) REVERT: A 173 ARG cc_start: 0.7414 (mmt180) cc_final: 0.7177 (ttm-80) REVERT: A 316 LYS cc_start: 0.9316 (mtmm) cc_final: 0.9116 (mtmm) REVERT: C 410 TYR cc_start: 0.7999 (m-10) cc_final: 0.7688 (m-80) REVERT: E 316 LYS cc_start: 0.9564 (mtmm) cc_final: 0.9216 (ptpp) REVERT: F 262 GLU cc_start: 0.8677 (tp30) cc_final: 0.8399 (tp30) outliers start: 3 outliers final: 1 residues processed: 106 average time/residue: 0.5284 time to fit residues: 82.7942 Evaluate side-chains 97 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 116 optimal weight: 0.1980 chunk 71 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 84 optimal weight: 0.0980 chunk 132 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 252 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 194 GLN A 205 GLN C 397 ASN C 523 ASN D 397 ASN ** D 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 ASN F 523 ASN F 567 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.095574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.058866 restraints weight = 57679.797| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.85 r_work: 0.2652 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22401 Z= 0.191 Angle : 0.605 10.033 30476 Z= 0.308 Chirality : 0.041 0.184 3356 Planarity : 0.005 0.067 4049 Dihedral : 4.121 43.483 3142 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.89 % Favored : 93.97 % Rotamer: Outliers : 2.23 % Allowed : 18.81 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2784 helix: 1.71 (0.15), residues: 1344 sheet: -1.24 (0.34), residues: 226 loop : -1.58 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 85 HIS 0.004 0.001 HIS A 427 PHE 0.040 0.002 PHE A 76 TYR 0.012 0.001 TYR E 453 ARG 0.006 0.000 ARG D 354 Details of bonding type rmsd hydrogen bonds : bond 0.05254 ( 982) hydrogen bonds : angle 4.96793 ( 2850) covalent geometry : bond 0.00448 (22401) covalent geometry : angle 0.60541 (30476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 103 time to evaluate : 5.033 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 107 MET cc_start: 0.7503 (mmm) cc_final: 0.6906 (mmp) REVERT: A 173 ARG cc_start: 0.7698 (mmt180) cc_final: 0.7225 (ttm-80) REVERT: C 410 TYR cc_start: 0.8244 (m-10) cc_final: 0.7917 (m-80) REVERT: E 316 LYS cc_start: 0.9547 (mtmm) cc_final: 0.9272 (ptpp) REVERT: E 410 TYR cc_start: 0.8322 (p90) cc_final: 0.8040 (p90) REVERT: F 262 GLU cc_start: 0.8674 (tp30) cc_final: 0.8456 (tp30) REVERT: F 317 LEU cc_start: 0.9701 (OUTLIER) cc_final: 0.9315 (mt) REVERT: F 458 PHE cc_start: 0.9054 (m-10) cc_final: 0.8764 (m-80) outliers start: 50 outliers final: 23 residues processed: 148 average time/residue: 0.5876 time to fit residues: 131.2519 Evaluate side-chains 111 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 360 TYR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 407 SER Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 475 ASN Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 568 THR Chi-restraints excluded: chain F residue 588 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 62 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS F 471 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.095885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.059255 restraints weight = 57548.830| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.86 r_work: 0.2660 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22401 Z= 0.154 Angle : 0.571 9.614 30476 Z= 0.288 Chirality : 0.040 0.179 3356 Planarity : 0.005 0.058 4049 Dihedral : 3.971 22.223 3139 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.46 % Favored : 94.43 % Rotamer: Outliers : 2.41 % Allowed : 18.90 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2784 helix: 1.84 (0.15), residues: 1325 sheet: -1.01 (0.34), residues: 232 loop : -1.54 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 85 HIS 0.006 0.001 HIS A 156 PHE 0.025 0.001 PHE B 200 TYR 0.008 0.001 TYR E 360 ARG 0.005 0.000 ARG B 192 Details of bonding type rmsd hydrogen bonds : bond 0.04679 ( 982) hydrogen bonds : angle 4.68199 ( 2850) covalent geometry : bond 0.00358 (22401) covalent geometry : angle 0.57086 (30476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 103 time to evaluate : 2.709 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 100 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7877 (tt) REVERT: A 107 MET cc_start: 0.7374 (mmm) cc_final: 0.6793 (mmp) REVERT: A 173 ARG cc_start: 0.7728 (mmt180) cc_final: 0.7333 (ttm-80) REVERT: B 58 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6205 (mp) REVERT: C 410 TYR cc_start: 0.8189 (m-10) cc_final: 0.7765 (m-10) REVERT: E 316 LYS cc_start: 0.9519 (mtmm) cc_final: 0.9225 (ptpp) REVERT: E 410 TYR cc_start: 0.8274 (p90) cc_final: 0.8022 (p90) REVERT: F 317 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9329 (mt) REVERT: F 414 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8412 (tp) outliers start: 54 outliers final: 27 residues processed: 151 average time/residue: 0.4807 time to fit residues: 105.9035 Evaluate side-chains 118 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain C residue 360 TYR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 475 ASN Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 407 SER Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 475 ASN Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 497 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 0 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 chunk 263 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 253 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 257 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.057548 restraints weight = 58815.435| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.84 r_work: 0.2607 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 22401 Z= 0.263 Angle : 0.635 9.566 30476 Z= 0.319 Chirality : 0.043 0.189 3356 Planarity : 0.005 0.063 4049 Dihedral : 4.073 22.023 3139 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.36 % Favored : 93.57 % Rotamer: Outliers : 2.85 % Allowed : 18.99 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2784 helix: 1.73 (0.15), residues: 1318 sheet: -1.08 (0.33), residues: 233 loop : -1.55 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 85 HIS 0.005 0.001 HIS A 427 PHE 0.019 0.002 PHE F 454 TYR 0.009 0.001 TYR C 340 ARG 0.004 0.000 ARG B 192 Details of bonding type rmsd hydrogen bonds : bond 0.05606 ( 982) hydrogen bonds : angle 4.80298 ( 2850) covalent geometry : bond 0.00624 (22401) covalent geometry : angle 0.63484 (30476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 99 time to evaluate : 2.531 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 77 ARG cc_start: 0.9413 (tpm170) cc_final: 0.8789 (ttt-90) REVERT: A 100 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7773 (tt) REVERT: A 107 MET cc_start: 0.7380 (mmm) cc_final: 0.6702 (mmp) REVERT: B 44 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8164 (mt) REVERT: B 58 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6249 (mp) REVERT: B 82 MET cc_start: 0.9203 (tmm) cc_final: 0.8710 (tmm) REVERT: C 410 TYR cc_start: 0.8250 (m-10) cc_final: 0.7500 (m-10) REVERT: C 444 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6419 (t80) REVERT: E 410 TYR cc_start: 0.8361 (p90) cc_final: 0.8145 (p90) REVERT: F 317 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9399 (mt) REVERT: F 414 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8486 (tp) REVERT: F 458 PHE cc_start: 0.8824 (m-10) cc_final: 0.8436 (m-80) outliers start: 64 outliers final: 43 residues processed: 155 average time/residue: 0.4422 time to fit residues: 100.4497 Evaluate side-chains 143 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain C residue 360 TYR Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 444 TYR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 475 ASN Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 589 CYS Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 568 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 101 optimal weight: 0.7980 chunk 154 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.095471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.058809 restraints weight = 57941.864| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.84 r_work: 0.2648 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22401 Z= 0.142 Angle : 0.565 9.575 30476 Z= 0.283 Chirality : 0.040 0.178 3356 Planarity : 0.005 0.053 4049 Dihedral : 3.984 21.755 3139 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 2.41 % Allowed : 20.24 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.16), residues: 2784 helix: 1.82 (0.15), residues: 1332 sheet: -1.00 (0.34), residues: 233 loop : -1.50 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 85 HIS 0.003 0.001 HIS C 417 PHE 0.021 0.001 PHE F 454 TYR 0.010 0.001 TYR E 360 ARG 0.005 0.000 ARG F 404 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 982) hydrogen bonds : angle 4.50956 ( 2850) covalent geometry : bond 0.00333 (22401) covalent geometry : angle 0.56495 (30476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 97 time to evaluate : 2.410 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 100 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7823 (tt) REVERT: A 107 MET cc_start: 0.7330 (mmm) cc_final: 0.6643 (mmp) REVERT: B 44 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8208 (mt) REVERT: B 58 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6221 (mp) REVERT: B 82 MET cc_start: 0.9177 (tmm) cc_final: 0.8643 (tmm) REVERT: B 210 ARG cc_start: 0.9139 (tmm-80) cc_final: 0.8619 (tmm-80) REVERT: C 410 TYR cc_start: 0.8159 (m-10) cc_final: 0.7351 (m-10) REVERT: C 444 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.6369 (t80) REVERT: E 410 TYR cc_start: 0.8286 (p90) cc_final: 0.8073 (p90) REVERT: E 527 LYS cc_start: 0.8889 (tptp) cc_final: 0.8682 (tptp) REVERT: F 317 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9354 (mt) REVERT: F 414 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8408 (tp) outliers start: 54 outliers final: 35 residues processed: 142 average time/residue: 0.4241 time to fit residues: 89.6185 Evaluate side-chains 133 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain C residue 444 TYR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 475 ASN Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 407 SER Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 475 ASN Chi-restraints excluded: chain E residue 589 CYS Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 568 THR Chi-restraints excluded: chain F residue 588 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 161 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.094258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.057672 restraints weight = 58131.525| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.83 r_work: 0.2616 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 22401 Z= 0.238 Angle : 0.614 9.575 30476 Z= 0.308 Chirality : 0.042 0.186 3356 Planarity : 0.005 0.050 4049 Dihedral : 4.040 21.677 3139 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.43 % Rotamer: Outliers : 2.85 % Allowed : 19.97 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2784 helix: 1.76 (0.15), residues: 1327 sheet: -1.07 (0.34), residues: 233 loop : -1.47 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 85 HIS 0.004 0.001 HIS F 264 PHE 0.020 0.002 PHE F 454 TYR 0.008 0.001 TYR E 360 ARG 0.006 0.000 ARG F 620 Details of bonding type rmsd hydrogen bonds : bond 0.05231 ( 982) hydrogen bonds : angle 4.63542 ( 2850) covalent geometry : bond 0.00562 (22401) covalent geometry : angle 0.61443 (30476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 102 time to evaluate : 2.230 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 51 ARG cc_start: 0.9187 (mtp180) cc_final: 0.8954 (mtp85) REVERT: A 100 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7782 (tt) REVERT: A 107 MET cc_start: 0.7352 (mmm) cc_final: 0.6672 (mmp) REVERT: B 44 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8205 (mt) REVERT: B 48 PHE cc_start: 0.8634 (t80) cc_final: 0.8335 (m-10) REVERT: B 58 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6024 (mp) REVERT: B 82 MET cc_start: 0.9180 (tmm) cc_final: 0.8618 (tmm) REVERT: B 210 ARG cc_start: 0.9147 (tmm-80) cc_final: 0.8619 (tmm-80) REVERT: C 410 TYR cc_start: 0.8186 (m-10) cc_final: 0.7382 (m-10) REVERT: C 444 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.6400 (t80) REVERT: E 316 LYS cc_start: 0.9728 (mtpp) cc_final: 0.9368 (ptpp) REVERT: F 317 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9381 (mt) REVERT: F 414 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8492 (tp) outliers start: 64 outliers final: 46 residues processed: 156 average time/residue: 0.4677 time to fit residues: 107.2177 Evaluate side-chains 149 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain C residue 360 TYR Chi-restraints excluded: chain C residue 444 TYR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 475 ASN Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 475 ASN Chi-restraints excluded: chain E residue 589 CYS Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 568 THR Chi-restraints excluded: chain F residue 588 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 214 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.096389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.059637 restraints weight = 58059.269| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.89 r_work: 0.2671 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22401 Z= 0.108 Angle : 0.542 9.540 30476 Z= 0.272 Chirality : 0.039 0.179 3356 Planarity : 0.004 0.046 4049 Dihedral : 3.873 21.180 3139 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 2.45 % Allowed : 20.78 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2784 helix: 1.99 (0.15), residues: 1326 sheet: -0.95 (0.35), residues: 235 loop : -1.37 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 85 HIS 0.005 0.000 HIS A 33 PHE 0.025 0.001 PHE B 200 TYR 0.010 0.001 TYR E 410 ARG 0.005 0.000 ARG F 620 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 982) hydrogen bonds : angle 4.26262 ( 2850) covalent geometry : bond 0.00247 (22401) covalent geometry : angle 0.54228 (30476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 107 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.9197 (mtp180) cc_final: 0.8978 (mtp85) REVERT: A 77 ARG cc_start: 0.9369 (tpm170) cc_final: 0.8735 (ttt180) REVERT: A 100 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7873 (tt) REVERT: A 107 MET cc_start: 0.7175 (mmm) cc_final: 0.6501 (mmp) REVERT: B 58 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6077 (mp) REVERT: B 82 MET cc_start: 0.9240 (tmm) cc_final: 0.8775 (tmm) REVERT: B 210 ARG cc_start: 0.9142 (tmm-80) cc_final: 0.8603 (tmm-80) REVERT: C 410 TYR cc_start: 0.8080 (m-10) cc_final: 0.7244 (m-10) REVERT: C 444 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6289 (t80) REVERT: C 511 ASP cc_start: 0.9369 (m-30) cc_final: 0.8945 (m-30) REVERT: E 316 LYS cc_start: 0.9717 (mtpp) cc_final: 0.9344 (ptpp) REVERT: E 527 LYS cc_start: 0.8930 (tptp) cc_final: 0.8706 (tptp) REVERT: F 414 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8325 (tp) outliers start: 55 outliers final: 34 residues processed: 153 average time/residue: 0.4708 time to fit residues: 104.0206 Evaluate side-chains 133 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 444 TYR Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain C residue 444 TYR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 475 ASN Chi-restraints excluded: chain E residue 589 CYS Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 452 HIS Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 568 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 168 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 208 optimal weight: 0.0570 chunk 108 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.096691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.060202 restraints weight = 57500.422| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.83 r_work: 0.2687 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22401 Z= 0.105 Angle : 0.541 9.454 30476 Z= 0.268 Chirality : 0.039 0.172 3356 Planarity : 0.004 0.047 4049 Dihedral : 3.775 20.628 3139 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.39 % Favored : 94.54 % Rotamer: Outliers : 2.41 % Allowed : 20.82 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2784 helix: 2.07 (0.15), residues: 1321 sheet: -0.94 (0.35), residues: 237 loop : -1.29 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 85 HIS 0.003 0.000 HIS A 417 PHE 0.022 0.001 PHE F 454 TYR 0.009 0.001 TYR E 410 ARG 0.012 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 982) hydrogen bonds : angle 4.17221 ( 2850) covalent geometry : bond 0.00241 (22401) covalent geometry : angle 0.54055 (30476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 103 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.9231 (mtp180) cc_final: 0.9010 (mtp85) REVERT: A 100 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7831 (tt) REVERT: A 172 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7816 (mtp180) REVERT: A 173 ARG cc_start: 0.7499 (mmt180) cc_final: 0.7038 (ttm-80) REVERT: B 44 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8102 (mt) REVERT: B 58 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6148 (mp) REVERT: B 82 MET cc_start: 0.9207 (tmm) cc_final: 0.8682 (tmm) REVERT: B 209 GLN cc_start: 0.9275 (pt0) cc_final: 0.9045 (pt0) REVERT: B 210 ARG cc_start: 0.9146 (tmm-80) cc_final: 0.8596 (tmm-80) REVERT: C 410 TYR cc_start: 0.8044 (m-10) cc_final: 0.7194 (m-10) REVERT: C 444 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.6270 (t80) REVERT: C 511 ASP cc_start: 0.9368 (m-30) cc_final: 0.8944 (m-30) REVERT: D 594 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7018 (mpt180) REVERT: E 316 LYS cc_start: 0.9704 (mtpp) cc_final: 0.9333 (ptpp) REVERT: F 414 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8320 (tp) outliers start: 54 outliers final: 37 residues processed: 146 average time/residue: 0.4341 time to fit residues: 92.3663 Evaluate side-chains 138 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 444 TYR Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain C residue 444 TYR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 475 ASN Chi-restraints excluded: chain E residue 589 CYS Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 452 HIS Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 568 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 254 optimal weight: 0.6980 chunk 114 optimal weight: 0.0980 chunk 148 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.096293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.059660 restraints weight = 57614.035| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.84 r_work: 0.2675 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22401 Z= 0.133 Angle : 0.548 10.113 30476 Z= 0.272 Chirality : 0.039 0.171 3356 Planarity : 0.004 0.048 4049 Dihedral : 3.761 20.697 3139 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.39 % Favored : 94.54 % Rotamer: Outliers : 2.10 % Allowed : 21.00 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2784 helix: 2.08 (0.15), residues: 1319 sheet: -0.92 (0.34), residues: 237 loop : -1.25 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 85 HIS 0.004 0.001 HIS D 462 PHE 0.028 0.001 PHE D 458 TYR 0.013 0.001 TYR A 453 ARG 0.010 0.000 ARG B 241 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 982) hydrogen bonds : angle 4.20133 ( 2850) covalent geometry : bond 0.00312 (22401) covalent geometry : angle 0.54770 (30476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 97 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.9266 (mtp180) cc_final: 0.8942 (mtt-85) REVERT: A 100 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7812 (tt) REVERT: A 172 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7813 (mtp180) REVERT: A 173 ARG cc_start: 0.7510 (mmt180) cc_final: 0.7073 (ttm-80) REVERT: B 58 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6100 (mp) REVERT: B 82 MET cc_start: 0.9202 (tmm) cc_final: 0.8672 (tmm) REVERT: B 209 GLN cc_start: 0.9269 (pt0) cc_final: 0.9041 (pt0) REVERT: B 210 ARG cc_start: 0.9158 (tmm-80) cc_final: 0.8609 (tmm-80) REVERT: C 316 LYS cc_start: 0.9647 (mmmm) cc_final: 0.9306 (mmtm) REVERT: C 410 TYR cc_start: 0.8066 (m-10) cc_final: 0.7242 (m-10) REVERT: C 444 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6208 (t80) REVERT: D 594 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7083 (mpt180) REVERT: E 316 LYS cc_start: 0.9707 (mtpp) cc_final: 0.9375 (ptpp) REVERT: E 410 TYR cc_start: 0.8168 (p90) cc_final: 0.7636 (p90) REVERT: F 262 GLU cc_start: 0.8619 (tp30) cc_final: 0.8345 (tp30) REVERT: F 414 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8337 (tp) REVERT: F 441 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7298 (mp) outliers start: 47 outliers final: 37 residues processed: 136 average time/residue: 0.4352 time to fit residues: 86.1221 Evaluate side-chains 139 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 444 TYR Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain C residue 444 TYR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 475 ASN Chi-restraints excluded: chain E residue 589 CYS Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 452 HIS Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 568 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 80 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 208 optimal weight: 0.1980 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 277 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.096224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.059557 restraints weight = 57871.626| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.86 r_work: 0.2671 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22401 Z= 0.129 Angle : 0.558 11.676 30476 Z= 0.276 Chirality : 0.039 0.171 3356 Planarity : 0.004 0.067 4049 Dihedral : 3.760 20.599 3139 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.35 % Favored : 94.58 % Rotamer: Outliers : 2.05 % Allowed : 21.04 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2784 helix: 2.08 (0.15), residues: 1320 sheet: -0.88 (0.34), residues: 237 loop : -1.23 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 85 HIS 0.004 0.001 HIS D 462 PHE 0.025 0.001 PHE D 458 TYR 0.009 0.001 TYR E 410 ARG 0.006 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 982) hydrogen bonds : angle 4.19309 ( 2850) covalent geometry : bond 0.00303 (22401) covalent geometry : angle 0.55763 (30476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 100 time to evaluate : 2.273 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 51 ARG cc_start: 0.9276 (mtp180) cc_final: 0.8948 (mtt-85) REVERT: A 100 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7852 (tt) REVERT: A 173 ARG cc_start: 0.7514 (mmt180) cc_final: 0.7121 (ttm-80) REVERT: B 58 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6209 (mp) REVERT: B 82 MET cc_start: 0.9196 (tmm) cc_final: 0.8677 (tmm) REVERT: B 209 GLN cc_start: 0.9276 (pt0) cc_final: 0.9050 (pt0) REVERT: B 210 ARG cc_start: 0.9159 (tmm-80) cc_final: 0.8609 (tmm-80) REVERT: C 316 LYS cc_start: 0.9646 (mmmm) cc_final: 0.9293 (mmtm) REVERT: C 410 TYR cc_start: 0.8055 (m-10) cc_final: 0.7225 (m-10) REVERT: C 444 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6224 (t80) REVERT: C 511 ASP cc_start: 0.9380 (m-30) cc_final: 0.8959 (m-30) REVERT: D 444 TYR cc_start: 0.6426 (t80) cc_final: 0.5605 (t80) REVERT: D 594 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7084 (mpt180) REVERT: E 316 LYS cc_start: 0.9708 (mtpp) cc_final: 0.9375 (ptpp) REVERT: E 410 TYR cc_start: 0.8175 (p90) cc_final: 0.7648 (p90) REVERT: F 262 GLU cc_start: 0.8640 (tp30) cc_final: 0.8398 (tp30) REVERT: F 414 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8340 (tp) REVERT: F 441 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7336 (mp) outliers start: 46 outliers final: 36 residues processed: 140 average time/residue: 0.4275 time to fit residues: 88.4901 Evaluate side-chains 140 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 444 TYR Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain C residue 444 TYR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 475 ASN Chi-restraints excluded: chain E residue 589 CYS Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 452 HIS Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 568 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 6 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 207 optimal weight: 0.0270 chunk 163 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 238 optimal weight: 4.9990 chunk 239 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.095233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.058400 restraints weight = 58178.916| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.87 r_work: 0.2637 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 22401 Z= 0.189 Angle : 0.590 11.774 30476 Z= 0.293 Chirality : 0.040 0.181 3356 Planarity : 0.004 0.049 4049 Dihedral : 3.841 20.948 3139 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 2.10 % Allowed : 21.09 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2784 helix: 2.00 (0.15), residues: 1326 sheet: -0.93 (0.33), residues: 249 loop : -1.24 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 85 HIS 0.003 0.001 HIS B 417 PHE 0.024 0.001 PHE D 458 TYR 0.010 0.001 TYR E 410 ARG 0.005 0.000 ARG D 385 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 982) hydrogen bonds : angle 4.34399 ( 2850) covalent geometry : bond 0.00447 (22401) covalent geometry : angle 0.58997 (30476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11815.18 seconds wall clock time: 207 minutes 30.81 seconds (12450.81 seconds total)