Starting phenix.real_space_refine on Fri Sep 19 01:33:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z40_39759/09_2025/8z40_39759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z40_39759/09_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_39759/09_2025/8z40_39759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z40_39759/09_2025/8z40_39759.map" model { file = "/net/cci-nas-00/data/ceres_data/8z40_39759/09_2025/8z40_39759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z40_39759/09_2025/8z40_39759.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.37, per 1000 atoms: 0.25 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: 1.90 Conformation dependent library (CDL) restraints added in 916.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.97 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: 3.99 Time building geometry restraints manager: 2.51 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.880 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (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 ARG 0.012 0.000 ARG A 173 TYR 0.013 0.001 TYR C 410 PHE 0.028 0.002 PHE D 458 TRP 0.063 0.002 TRP A 85 HIS 0.005 0.001 HIS D 462 Details of bonding type rmsd covalent geometry : bond 0.00283 (22401) covalent geometry : angle 0.66294 (30476) hydrogen bonds : bond 0.18405 ( 982) hydrogen bonds : angle 6.26609 ( 2850) *********************** 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 : 0.891 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: 0.2340 time to fit residues: 35.5041 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 : 0.867 ------------------------------------------------------------------------------- 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 197 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 B 523 ASN 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 = 0.3593 r_free = 0.3593 target = 0.093720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.056880 restraints weight = 58870.798| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.86 r_work: 0.2592 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 22401 Z= 0.330 Angle : 0.709 9.547 30476 Z= 0.360 Chirality : 0.045 0.198 3356 Planarity : 0.006 0.076 4049 Dihedral : 4.330 43.952 3142 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.00 % Favored : 92.85 % Rotamer: Outliers : 2.72 % Allowed : 18.72 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.16), residues: 2784 helix: 1.48 (0.15), residues: 1334 sheet: -1.36 (0.34), residues: 221 loop : -1.65 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.017 0.002 TYR E 453 PHE 0.038 0.002 PHE A 76 TRP 0.042 0.002 TRP A 85 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00775 (22401) covalent geometry : angle 0.70927 (30476) hydrogen bonds : bond 0.06640 ( 982) hydrogen bonds : angle 5.24465 ( 2850) *********************** 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 163 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 102 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7822 (tt) REVERT: A 107 MET cc_start: 0.7560 (mmm) cc_final: 0.6936 (mmp) REVERT: C 410 TYR cc_start: 0.8300 (m-10) cc_final: 0.7976 (m-80) REVERT: E 316 LYS cc_start: 0.9562 (mtmm) cc_final: 0.9279 (ptpp) REVERT: E 410 TYR cc_start: 0.8393 (p90) cc_final: 0.8146 (p90) REVERT: F 317 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9409 (mt) REVERT: F 414 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8536 (tp) REVERT: F 458 PHE cc_start: 0.9129 (m-10) cc_final: 0.8816 (m-80) outliers start: 61 outliers final: 31 residues processed: 158 average time/residue: 0.2040 time to fit residues: 47.2059 Evaluate side-chains 127 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 240 LEU 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 100 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 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 401 ILE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 593 THR 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 235 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 218 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 221 optimal weight: 0.0040 chunk 201 optimal weight: 9.9990 chunk 215 optimal weight: 0.7980 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 273 HIS B 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.095719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.059082 restraints weight = 57692.729| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.87 r_work: 0.2654 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22401 Z= 0.137 Angle : 0.570 9.593 30476 Z= 0.289 Chirality : 0.040 0.177 3356 Planarity : 0.005 0.058 4049 Dihedral : 4.076 22.416 3139 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.39 % Favored : 94.50 % Rotamer: Outliers : 2.36 % Allowed : 18.99 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.16), residues: 2784 helix: 1.73 (0.15), residues: 1329 sheet: -1.18 (0.32), residues: 251 loop : -1.59 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 620 TYR 0.008 0.001 TYR E 410 PHE 0.026 0.001 PHE B 200 TRP 0.026 0.001 TRP A 85 HIS 0.009 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00316 (22401) covalent geometry : angle 0.57042 (30476) hydrogen bonds : bond 0.04626 ( 982) hydrogen bonds : angle 4.68385 ( 2850) *********************** 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 161 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 108 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7809 (tt) REVERT: A 107 MET cc_start: 0.7403 (mmm) cc_final: 0.6833 (mmp) REVERT: B 58 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6203 (mp) REVERT: B 210 ARG cc_start: 0.9120 (tmm-80) cc_final: 0.8606 (tmm-80) REVERT: C 410 TYR cc_start: 0.8204 (m-10) cc_final: 0.7499 (m-10) REVERT: C 444 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6307 (t80) REVERT: E 316 LYS cc_start: 0.9531 (mtmm) cc_final: 0.9223 (ptpp) REVERT: E 410 TYR cc_start: 0.8261 (p90) cc_final: 0.8031 (p90) REVERT: E 426 GLU cc_start: 0.9054 (tp30) cc_final: 0.8747 (tp30) REVERT: E 527 LYS cc_start: 0.8886 (tptp) cc_final: 0.8662 (tptp) REVERT: F 414 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8389 (tp) outliers start: 53 outliers final: 25 residues processed: 154 average time/residue: 0.1934 time to fit residues: 43.5978 Evaluate side-chains 118 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU 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 240 LEU Chi-restraints excluded: chain B residue 363 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 593 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 407 SER 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 414 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 588 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 60 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 chunk 270 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.057335 restraints weight = 58289.615| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.86 r_work: 0.2609 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1452 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= 0.236 Angle : 0.620 9.576 30476 Z= 0.311 Chirality : 0.042 0.187 3356 Planarity : 0.005 0.065 4049 Dihedral : 4.101 22.056 3139 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.43 % Rotamer: Outliers : 2.94 % Allowed : 19.53 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.16), residues: 2784 helix: 1.68 (0.15), residues: 1322 sheet: -1.15 (0.33), residues: 239 loop : -1.56 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 512 TYR 0.009 0.001 TYR E 360 PHE 0.020 0.002 PHE F 454 TRP 0.021 0.001 TRP A 85 HIS 0.006 0.001 HIS F 264 Details of bonding type rmsd covalent geometry : bond 0.00559 (22401) covalent geometry : angle 0.61966 (30476) hydrogen bonds : bond 0.05490 ( 982) hydrogen bonds : angle 4.76001 ( 2850) *********************** 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 167 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 101 time to evaluate : 0.772 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 100 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7840 (tt) REVERT: A 107 MET cc_start: 0.7350 (mmm) cc_final: 0.6681 (mmp) REVERT: A 172 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8260 (ptt180) REVERT: B 44 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8177 (mm) REVERT: B 58 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6133 (mp) REVERT: B 82 MET cc_start: 0.9235 (tmm) cc_final: 0.8769 (tmm) REVERT: B 210 ARG cc_start: 0.9138 (tmm-80) cc_final: 0.8608 (tmm-80) REVERT: C 410 TYR cc_start: 0.8229 (m-10) cc_final: 0.7492 (m-10) REVERT: C 444 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.6433 (t80) REVERT: E 410 TYR cc_start: 0.8338 (p90) cc_final: 0.8137 (p90) REVERT: F 317 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9364 (mt) REVERT: F 414 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8499 (tp) REVERT: F 458 PHE cc_start: 0.8784 (m-10) cc_final: 0.8422 (m-80) outliers start: 66 outliers final: 40 residues processed: 160 average time/residue: 0.2026 time to fit residues: 47.2225 Evaluate side-chains 143 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 96 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 172 ARG 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 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 100 LEU 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 562 VAL 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 242 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 138 optimal weight: 0.0470 chunk 208 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.095525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.058808 restraints weight = 58205.049| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.86 r_work: 0.2645 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22401 Z= 0.139 Angle : 0.560 9.555 30476 Z= 0.280 Chirality : 0.040 0.177 3356 Planarity : 0.005 0.051 4049 Dihedral : 3.974 21.720 3139 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.35 % Favored : 94.58 % Rotamer: Outliers : 2.41 % Allowed : 20.51 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.16), residues: 2784 helix: 1.83 (0.15), residues: 1332 sheet: -1.08 (0.33), residues: 240 loop : -1.49 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 512 TYR 0.008 0.001 TYR E 410 PHE 0.021 0.001 PHE F 454 TRP 0.021 0.001 TRP A 85 HIS 0.003 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00328 (22401) covalent geometry : angle 0.55986 (30476) hydrogen bonds : bond 0.04263 ( 982) hydrogen bonds : angle 4.45670 ( 2850) *********************** 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 : 0.899 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 100 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7855 (tt) REVERT: A 107 MET cc_start: 0.7330 (mmm) cc_final: 0.6717 (mmp) REVERT: A 172 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8279 (ptt180) REVERT: B 44 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8240 (mt) REVERT: B 48 PHE cc_start: 0.8677 (t80) cc_final: 0.8342 (m-10) REVERT: B 58 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.5988 (mp) REVERT: B 82 MET cc_start: 0.9175 (tmm) cc_final: 0.8628 (tmm) REVERT: B 210 ARG cc_start: 0.9138 (tmm-80) cc_final: 0.8616 (tmm-80) REVERT: C 410 TYR cc_start: 0.8126 (m-10) cc_final: 0.7313 (m-10) REVERT: C 444 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6318 (t80) REVERT: E 316 LYS cc_start: 0.9719 (mtpp) cc_final: 0.9351 (ptpp) REVERT: E 410 TYR cc_start: 0.8251 (p90) cc_final: 0.8047 (p90) REVERT: E 527 LYS cc_start: 0.8935 (tptp) cc_final: 0.8690 (tptp) REVERT: F 262 GLU cc_start: 0.8654 (tp30) cc_final: 0.8436 (tp30) REVERT: F 317 LEU cc_start: 0.9692 (OUTLIER) cc_final: 0.9327 (mt) REVERT: F 414 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8377 (tp) outliers start: 54 outliers final: 34 residues processed: 145 average time/residue: 0.2110 time to fit residues: 45.1264 Evaluate side-chains 134 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 172 ARG 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 220 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 363 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 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 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 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 568 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 153 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 145 optimal weight: 0.0670 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 395 HIS F 614 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.094986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.057010 restraints weight = 58106.038| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 4.03 r_work: 0.2609 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 22401 Z= 0.281 Angle : 0.652 9.596 30476 Z= 0.326 Chirality : 0.043 0.191 3356 Planarity : 0.005 0.051 4049 Dihedral : 4.113 21.944 3139 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 3.66 % Allowed : 19.97 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.16), residues: 2784 helix: 1.69 (0.15), residues: 1315 sheet: -1.23 (0.33), residues: 239 loop : -1.52 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 512 TYR 0.012 0.001 TYR E 360 PHE 0.019 0.002 PHE F 454 TRP 0.027 0.001 TRP A 85 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00662 (22401) covalent geometry : angle 0.65167 (30476) hydrogen bonds : bond 0.05784 ( 982) hydrogen bonds : angle 4.76354 ( 2850) *********************** 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 185 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 103 time to evaluate : 0.765 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: 0.9183 (mtp180) cc_final: 0.8945 (mtp85) REVERT: A 100 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7698 (tt) REVERT: A 107 MET cc_start: 0.7266 (mmm) cc_final: 0.6656 (mmp) REVERT: A 172 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8296 (ptt180) REVERT: B 58 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6132 (mp) REVERT: B 82 MET cc_start: 0.9196 (tmm) cc_final: 0.8654 (tmm) REVERT: B 210 ARG cc_start: 0.9160 (tmm-80) cc_final: 0.8627 (tmm-80) REVERT: B 289 LYS cc_start: 0.9593 (OUTLIER) cc_final: 0.9317 (mtmm) REVERT: C 410 TYR cc_start: 0.8195 (m-10) cc_final: 0.7351 (m-10) REVERT: C 444 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.6400 (t80) REVERT: E 316 LYS cc_start: 0.9753 (mtpp) cc_final: 0.9377 (ptpp) REVERT: F 262 GLU cc_start: 0.8775 (tp30) cc_final: 0.8495 (tp30) REVERT: F 317 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9371 (mt) REVERT: F 414 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8426 (tp) outliers start: 82 outliers final: 56 residues processed: 175 average time/residue: 0.1953 time to fit residues: 49.7545 Evaluate side-chains 160 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 97 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 172 ARG Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 317 LEU 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 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 47 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 140 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 317 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 519 CYS 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 317 LEU 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 D residue 558 LEU 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 E residue 593 THR 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 360 TYR Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 568 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 16 optimal weight: 1.9990 chunk 105 optimal weight: 0.0040 chunk 177 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 134 optimal weight: 0.0970 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.096125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.059450 restraints weight = 58032.385| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.87 r_work: 0.2664 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22401 Z= 0.108 Angle : 0.550 9.529 30476 Z= 0.276 Chirality : 0.039 0.168 3356 Planarity : 0.004 0.045 4049 Dihedral : 3.914 21.468 3139 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.10 % Favored : 94.83 % Rotamer: Outliers : 2.63 % Allowed : 20.95 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.17), residues: 2784 helix: 1.90 (0.15), residues: 1333 sheet: -1.06 (0.34), residues: 241 loop : -1.37 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 620 TYR 0.017 0.001 TYR C 453 PHE 0.049 0.001 PHE B 200 TRP 0.023 0.001 TRP A 85 HIS 0.006 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00242 (22401) covalent geometry : angle 0.54989 (30476) hydrogen bonds : bond 0.03742 ( 982) hydrogen bonds : angle 4.30725 ( 2850) *********************** 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 167 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 108 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.9200 (mtp180) cc_final: 0.8990 (mtp85) REVERT: A 100 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7801 (tt) REVERT: A 172 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8311 (ptt180) REVERT: B 48 PHE cc_start: 0.8592 (t80) cc_final: 0.8385 (m-80) REVERT: B 82 MET cc_start: 0.9231 (tmm) cc_final: 0.8772 (tmm) REVERT: B 210 ARG cc_start: 0.9144 (tmm-80) cc_final: 0.8601 (tmm-80) REVERT: C 410 TYR cc_start: 0.8059 (m-10) cc_final: 0.7201 (m-10) REVERT: C 444 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6283 (t80) REVERT: C 511 ASP cc_start: 0.9375 (m-30) cc_final: 0.8953 (m-30) REVERT: D 594 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7442 (mpt180) REVERT: E 316 LYS cc_start: 0.9730 (mtpp) cc_final: 0.9356 (ptpp) REVERT: E 410 TYR cc_start: 0.8114 (p90) cc_final: 0.7600 (p90) REVERT: E 527 LYS cc_start: 0.8927 (tptp) cc_final: 0.8679 (tptp) REVERT: F 414 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8336 (tp) outliers start: 59 outliers final: 38 residues processed: 158 average time/residue: 0.1958 time to fit residues: 45.2959 Evaluate side-chains 140 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 172 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 469 THR 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 86 PHE 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 461 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 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 475 ASN Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 594 ARG 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 12 optimal weight: 6.9990 chunk 274 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 21 optimal weight: 0.0170 chunk 214 optimal weight: 0.0170 chunk 113 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 154 optimal weight: 3.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.096970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.060165 restraints weight = 57702.954| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.89 r_work: 0.2690 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22401 Z= 0.102 Angle : 0.549 10.480 30476 Z= 0.271 Chirality : 0.039 0.173 3356 Planarity : 0.004 0.046 4049 Dihedral : 3.767 20.239 3139 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 2.01 % Allowed : 21.71 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.17), residues: 2784 helix: 2.05 (0.15), residues: 1326 sheet: -1.00 (0.34), residues: 243 loop : -1.27 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 354 TYR 0.020 0.001 TYR C 453 PHE 0.043 0.001 PHE B 200 TRP 0.021 0.001 TRP A 85 HIS 0.004 0.000 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00231 (22401) covalent geometry : angle 0.54899 (30476) hydrogen bonds : bond 0.03357 ( 982) hydrogen bonds : angle 4.14045 ( 2850) *********************** 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 146 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 101 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.9253 (mtp180) cc_final: 0.9052 (mtp85) REVERT: A 172 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8337 (ptt180) REVERT: B 58 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.5894 (mp) REVERT: B 82 MET cc_start: 0.9190 (tmm) cc_final: 0.8673 (tmm) REVERT: B 210 ARG cc_start: 0.9137 (tmm-80) cc_final: 0.8598 (tmm-80) REVERT: C 316 LYS cc_start: 0.9650 (mmmm) cc_final: 0.9307 (mmtm) REVERT: C 410 TYR cc_start: 0.8007 (m-10) cc_final: 0.7146 (m-10) REVERT: C 444 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.6303 (t80) REVERT: C 511 ASP cc_start: 0.9364 (m-30) cc_final: 0.8940 (m-30) REVERT: D 594 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7372 (mpt180) REVERT: E 316 LYS cc_start: 0.9714 (mtpp) cc_final: 0.9366 (ptpp) REVERT: E 410 TYR cc_start: 0.8142 (p90) cc_final: 0.7614 (p90) REVERT: F 620 ARG cc_start: 0.8510 (tmm160) cc_final: 0.8125 (ttp80) outliers start: 45 outliers final: 35 residues processed: 139 average time/residue: 0.2226 time to fit residues: 44.3764 Evaluate side-chains 134 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 95 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 172 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 469 THR 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 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 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 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 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 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 161 optimal weight: 0.9990 chunk 276 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 195 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.095955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.059001 restraints weight = 58246.465| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.92 r_work: 0.2659 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22401 Z= 0.141 Angle : 0.559 11.460 30476 Z= 0.277 Chirality : 0.040 0.177 3356 Planarity : 0.004 0.047 4049 Dihedral : 3.774 20.538 3139 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 2.05 % Allowed : 21.80 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.17), residues: 2784 helix: 2.00 (0.15), residues: 1339 sheet: -0.99 (0.33), residues: 255 loop : -1.24 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 241 TYR 0.018 0.001 TYR C 453 PHE 0.032 0.001 PHE B 200 TRP 0.019 0.001 TRP A 85 HIS 0.004 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00334 (22401) covalent geometry : angle 0.55912 (30476) hydrogen bonds : bond 0.03891 ( 982) hydrogen bonds : angle 4.20193 ( 2850) *********************** 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 145 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 99 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.9272 (mtp180) cc_final: 0.8975 (mtt-85) REVERT: A 172 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8323 (ptt180) REVERT: B 82 MET cc_start: 0.9186 (tmm) cc_final: 0.8672 (tmm) REVERT: B 210 ARG cc_start: 0.9151 (tmm-80) cc_final: 0.8610 (tmm-80) REVERT: C 316 LYS cc_start: 0.9656 (mmmm) cc_final: 0.9309 (mmtm) REVERT: C 410 TYR cc_start: 0.8070 (m-10) cc_final: 0.7212 (m-10) REVERT: C 444 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6196 (t80) REVERT: C 511 ASP cc_start: 0.9383 (m-30) cc_final: 0.8964 (m-30) REVERT: E 316 LYS cc_start: 0.9719 (mtpp) cc_final: 0.9390 (ptpp) REVERT: E 410 TYR cc_start: 0.8175 (p90) cc_final: 0.7656 (p90) REVERT: F 262 GLU cc_start: 0.8623 (tp30) cc_final: 0.8350 (tp30) outliers start: 46 outliers final: 37 residues processed: 139 average time/residue: 0.2200 time to fit residues: 44.3299 Evaluate side-chains 134 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 95 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 172 ARG 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 86 PHE 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 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 449 THR Chi-restraints excluded: chain D residue 475 ASN 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 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 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 452 HIS Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 532 ASP 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 12 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.096014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.059200 restraints weight = 57890.270| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.86 r_work: 0.2661 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22401 Z= 0.134 Angle : 0.571 12.651 30476 Z= 0.281 Chirality : 0.039 0.175 3356 Planarity : 0.004 0.063 4049 Dihedral : 3.788 20.662 3139 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.43 % Rotamer: Outliers : 1.78 % Allowed : 21.93 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.17), residues: 2784 helix: 1.98 (0.15), residues: 1340 sheet: -0.94 (0.34), residues: 243 loop : -1.22 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 385 TYR 0.016 0.001 TYR C 453 PHE 0.030 0.001 PHE B 200 TRP 0.021 0.001 TRP A 85 HIS 0.004 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00317 (22401) covalent geometry : angle 0.57103 (30476) hydrogen bonds : bond 0.03872 ( 982) hydrogen bonds : angle 4.19427 ( 2850) ********************** 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 139 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.9276 (mtp180) cc_final: 0.8956 (mtt-85) REVERT: A 172 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8342 (ptt180) REVERT: B 82 MET cc_start: 0.9171 (tmm) cc_final: 0.8658 (tmm) REVERT: B 210 ARG cc_start: 0.9153 (tmm-80) cc_final: 0.8609 (tmm-80) REVERT: C 316 LYS cc_start: 0.9658 (mmmm) cc_final: 0.9308 (mmtm) REVERT: C 410 TYR cc_start: 0.8057 (m-10) cc_final: 0.7172 (m-10) REVERT: C 444 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6076 (t80) REVERT: C 511 ASP cc_start: 0.9382 (m-30) cc_final: 0.8961 (m-30) REVERT: E 316 LYS cc_start: 0.9713 (mtpp) cc_final: 0.9405 (ptpp) REVERT: E 410 TYR cc_start: 0.8191 (p90) cc_final: 0.7678 (p90) REVERT: F 262 GLU cc_start: 0.8646 (tp30) cc_final: 0.8401 (tp30) outliers start: 40 outliers final: 34 residues processed: 132 average time/residue: 0.2123 time to fit residues: 40.9515 Evaluate side-chains 134 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 111 MET Chi-restraints excluded: chain A residue 172 ARG 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 86 PHE Chi-restraints excluded: chain B residue 240 LEU 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 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 449 THR Chi-restraints excluded: chain D residue 475 ASN 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 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 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 239 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3625 r_free = 0.3625 target = 0.095434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.058556 restraints weight = 57947.110| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.88 r_work: 0.2642 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22401 Z= 0.171 Angle : 0.591 12.504 30476 Z= 0.291 Chirality : 0.040 0.181 3356 Planarity : 0.004 0.048 4049 Dihedral : 3.812 20.952 3139 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.25 % Rotamer: Outliers : 1.78 % Allowed : 21.93 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.17), residues: 2784 helix: 1.96 (0.15), residues: 1340 sheet: -0.97 (0.33), residues: 253 loop : -1.22 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 46 TYR 0.025 0.001 TYR C 453 PHE 0.031 0.001 PHE C 458 TRP 0.019 0.001 TRP A 85 HIS 0.004 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00405 (22401) covalent geometry : angle 0.59142 (30476) hydrogen bonds : bond 0.04342 ( 982) hydrogen bonds : angle 4.27251 ( 2850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5638.49 seconds wall clock time: 97 minutes 3.72 seconds (5823.72 seconds total)