Starting phenix.real_space_refine on Mon May 26 03:56:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k94_36974/05_2025/8k94_36974.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k94_36974/05_2025/8k94_36974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k94_36974/05_2025/8k94_36974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k94_36974/05_2025/8k94_36974.map" model { file = "/net/cci-nas-00/data/ceres_data/8k94_36974/05_2025/8k94_36974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k94_36974/05_2025/8k94_36974.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.030 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 38 5.16 5 C 17625 2.51 5 N 5000 2.21 5 O 5224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.75s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27890 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "D" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.74, per 1000 atoms: 0.60 Number of scatterers: 27890 At special positions: 0 Unit cell: (150.06, 138.58, 158.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 3 15.00 O 5224 8.00 N 5000 7.00 C 17625 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: 7.23 Conformation dependent library (CDL) restraints added in 3.6 seconds 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6600 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 48 sheets defined 54.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.659A pdb=" N LEU A 8 " --> pdb=" O SER A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.927A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 111 through 118 Processing helix chain 'A' and resid 121 through 154 Processing helix chain 'A' and resid 173 through 221 removed outlier: 3.607A pdb=" N ALA A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 363 through 369 removed outlier: 4.018A pdb=" N GLY A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.636A pdb=" N SER A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 407 Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 436 through 452 Processing helix chain 'A' and resid 456 through 471 removed outlier: 4.028A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 532 through 540 removed outlier: 3.741A pdb=" N ALA A 535 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY A 536 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU A 537 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 557 removed outlier: 3.524A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 597 Processing helix chain 'A' and resid 621 through 637 removed outlier: 3.549A pdb=" N LYS A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 651 No H-bonds generated for 'chain 'A' and resid 649 through 651' Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 removed outlier: 3.518A pdb=" N ALA A 680 " --> pdb=" O THR A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 719 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.689A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 111 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 121 through 153 Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.224A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.645A pdb=" N GLY B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.700A pdb=" N SER B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 407 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 451 Processing helix chain 'B' and resid 456 through 471 removed outlier: 4.064A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.975A pdb=" N GLY B 539 " --> pdb=" O GLY B 536 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B 540 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 541 " --> pdb=" O GLY B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'B' and resid 621 through 637 Processing helix chain 'B' and resid 649 through 654 removed outlier: 4.019A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 654 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 719 removed outlier: 3.640A pdb=" N GLU B 719 " --> pdb=" O LYS B 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 69 removed outlier: 3.686A pdb=" N THR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 111 Processing helix chain 'C' and resid 111 through 119 removed outlier: 3.870A pdb=" N PHE C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 154 Processing helix chain 'C' and resid 173 through 221 removed outlier: 4.175A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 242 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.969A pdb=" N GLN C 306 " --> pdb=" O HIS C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.677A pdb=" N GLY C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 380 removed outlier: 3.598A pdb=" N SER C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 408 Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 436 through 451 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.976A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 536 through 541 removed outlier: 4.267A pdb=" N GLY C 539 " --> pdb=" O GLY C 536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 540 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 557 removed outlier: 3.511A pdb=" N TYR C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 597 Processing helix chain 'C' and resid 621 through 637 Processing helix chain 'C' and resid 649 through 654 removed outlier: 4.280A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 654 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 694 through 719 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 69 removed outlier: 3.587A pdb=" N THR D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 111 removed outlier: 4.402A pdb=" N HIS D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 121 through 153 Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.269A pdb=" N ALA D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 242 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 273 through 279 Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.712A pdb=" N GLU D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 380 removed outlier: 3.717A pdb=" N SER D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 407 Processing helix chain 'D' and resid 412 through 428 Processing helix chain 'D' and resid 436 through 451 Processing helix chain 'D' and resid 456 through 471 removed outlier: 4.254A pdb=" N SER D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 532 through 535 removed outlier: 3.721A pdb=" N ALA D 535 " --> pdb=" O ASP D 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 532 through 535' Processing helix chain 'D' and resid 544 through 557 removed outlier: 3.525A pdb=" N TYR D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 597 Processing helix chain 'D' and resid 621 through 636 Processing helix chain 'D' and resid 649 through 654 removed outlier: 4.183A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 654 " --> pdb=" O LEU D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 719 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.595A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 121 through 154 Processing helix chain 'E' and resid 173 through 221 removed outlier: 5.438A pdb=" N ALA E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 246 through 251 removed outlier: 4.099A pdb=" N ARG E 251 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 363 through 367 Processing helix chain 'E' and resid 373 through 380 removed outlier: 3.918A pdb=" N SER E 377 " --> pdb=" O ASP E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 407 Processing helix chain 'E' and resid 412 through 427 Processing helix chain 'E' and resid 436 through 452 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.950A pdb=" N SER E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 535 through 540 removed outlier: 3.749A pdb=" N GLN E 540 " --> pdb=" O LEU E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 557 Processing helix chain 'E' and resid 585 through 597 Processing helix chain 'E' and resid 621 through 637 Processing helix chain 'E' and resid 649 through 654 removed outlier: 4.354A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU E 654 " --> pdb=" O LEU E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 269 removed outlier: 4.507A pdb=" N ASP A 313 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N HIS A 48 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 382 " --> pdb=" O HIS A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 254 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.522A pdb=" N ALA A 156 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA7, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AA8, first strand: chain 'A' and resid 529 through 530 removed outlier: 7.202A pdb=" N ILE A 529 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N PHE A 571 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N GLU A 498 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N VAL A 606 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASN A 500 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 644 " --> pdb=" O TYR A 672 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 674 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 609 through 610 removed outlier: 3.667A pdb=" N ALA A 609 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 266 through 269 removed outlier: 4.370A pdb=" N ASP B 313 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 312 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N HIS B 48 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ALA B 384 " --> pdb=" O HIS B 48 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR B 50 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 253 through 254 Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.558A pdb=" N ALA B 156 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AB5, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AB6, first strand: chain 'B' and resid 410 through 411 removed outlier: 7.114A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AB8, first strand: chain 'B' and resid 528 through 530 removed outlier: 6.838A pdb=" N ILE B 529 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N PHE B 571 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N GLU B 498 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N VAL B 606 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN B 500 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL B 644 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL B 674 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 609 through 610 Processing sheet with id=AC1, first strand: chain 'C' and resid 2 through 3 removed outlier: 4.726A pdb=" N ILE C 671 " --> pdb=" O LEU C 3 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N GLU C 498 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N VAL C 606 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN C 500 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 567 " --> pdb=" O HIS C 527 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 266 through 269 removed outlier: 4.156A pdb=" N ASP C 313 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 312 " --> pdb=" O ILE C 359 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 253 through 254 Processing sheet with id=AC4, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AC5, first strand: chain 'C' and resid 279 through 281 Processing sheet with id=AC6, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AC7, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AC8, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AC9, first strand: chain 'C' and resid 583 through 584 removed outlier: 4.240A pdb=" N ALA C 583 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 266 through 269 removed outlier: 4.380A pdb=" N ASP D 313 " --> pdb=" O GLU D 269 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD3, first strand: chain 'D' and resid 156 through 159 Processing sheet with id=AD4, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AD5, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AD6, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AD7, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AD8, first strand: chain 'D' and resid 498 through 504 removed outlier: 6.748A pdb=" N ILE D 529 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N PHE D 571 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 583 through 584 removed outlier: 4.568A pdb=" N ALA D 583 " --> pdb=" O VAL D 610 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 610 " --> pdb=" O ALA D 583 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 604 through 606 removed outlier: 6.409A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 266 through 268 removed outlier: 6.489A pdb=" N VAL E 267 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASP E 313 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU E 310 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL E 361 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU E 312 " --> pdb=" O VAL E 361 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 253 through 256 removed outlier: 7.581A pdb=" N LEU E 78 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AE5, first strand: chain 'E' and resid 280 through 281 Processing sheet with id=AE6, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AE7, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AE8, first strand: chain 'E' and resid 410 through 411 removed outlier: 7.247A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AF1, first strand: chain 'E' and resid 498 through 505 removed outlier: 3.742A pdb=" N TRP E 511 " --> pdb=" O VAL E 505 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 583 through 584 removed outlier: 4.235A pdb=" N ALA E 583 " --> pdb=" O VAL E 610 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 604 through 606 removed outlier: 6.125A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) 1588 hydrogen bonds defined for protein. 4587 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: 11.42 Time building geometry restraints manager: 8.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 9778 1.36 - 1.51: 7499 1.51 - 1.65: 11101 1.65 - 1.80: 49 1.80 - 1.95: 15 Bond restraints: 28442 Sorted by residual: bond pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 2.275 1.946 0.329 2.00e-02 2.50e+03 2.70e+02 bond pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" P TS6 B 801 " pdb=" S2P TS6 B 801 " ideal model delta sigma weight residual 2.275 1.948 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" CG PRO E 247 " pdb=" CD PRO E 247 " ideal model delta sigma weight residual 1.503 1.337 0.166 3.40e-02 8.65e+02 2.40e+01 bond pdb=" O4P TS6 C 801 " pdb=" P TS6 C 801 " ideal model delta sigma weight residual 1.516 1.613 -0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 28437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 38429 3.44 - 6.88: 167 6.88 - 10.32: 7 10.32 - 13.76: 9 13.76 - 17.20: 6 Bond angle restraints: 38618 Sorted by residual: angle pdb=" CA PRO E 247 " pdb=" N PRO E 247 " pdb=" CD PRO E 247 " ideal model delta sigma weight residual 112.00 96.80 15.20 1.40e+00 5.10e-01 1.18e+02 angle pdb=" N ARG E 203 " pdb=" CA ARG E 203 " pdb=" C ARG E 203 " ideal model delta sigma weight residual 114.62 106.34 8.28 1.14e+00 7.69e-01 5.28e+01 angle pdb=" N PRO E 247 " pdb=" CD PRO E 247 " pdb=" CG PRO E 247 " ideal model delta sigma weight residual 103.20 92.76 10.44 1.50e+00 4.44e-01 4.84e+01 angle pdb=" O1P TS6 C 801 " pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 98.15 115.35 -17.20 3.00e+00 1.11e-01 3.29e+01 angle pdb=" O1P TS6 D 801 " pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 98.15 115.34 -17.19 3.00e+00 1.11e-01 3.28e+01 ... (remaining 38613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15593 17.98 - 35.96: 1221 35.96 - 53.94: 237 53.94 - 71.93: 129 71.93 - 89.91: 85 Dihedral angle restraints: 17265 sinusoidal: 6990 harmonic: 10275 Sorted by residual: dihedral pdb=" CA ALA E 508 " pdb=" C ALA E 508 " pdb=" N PRO E 509 " pdb=" CA PRO E 509 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ALA A 508 " pdb=" C ALA A 508 " pdb=" N PRO A 509 " pdb=" CA PRO A 509 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ARG E 202 " pdb=" C ARG E 202 " pdb=" N ARG E 203 " pdb=" CA ARG E 203 " ideal model delta harmonic sigma weight residual 180.00 157.38 22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 17262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3854 0.065 - 0.130: 427 0.130 - 0.195: 20 0.195 - 0.261: 3 0.261 - 0.326: 1 Chirality restraints: 4305 Sorted by residual: chirality pdb=" CA PRO E 247 " pdb=" N PRO E 247 " pdb=" C PRO E 247 " pdb=" CB PRO E 247 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA TRP B 205 " pdb=" N TRP B 205 " pdb=" C TRP B 205 " pdb=" CB TRP B 205 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE B 558 " pdb=" CA ILE B 558 " pdb=" CG1 ILE B 558 " pdb=" CG2 ILE B 558 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 4302 not shown) Planarity restraints: 5155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 246 " 0.099 5.00e-02 4.00e+02 1.36e-01 2.98e+01 pdb=" N PRO E 247 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO E 247 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 247 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 205 " 0.037 2.00e-02 2.50e+03 2.72e-02 1.85e+01 pdb=" CG TRP B 205 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP B 205 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 205 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 205 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 205 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 205 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 205 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 205 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 205 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 205 " 0.024 2.00e-02 2.50e+03 2.22e-02 1.24e+01 pdb=" CG TRP A 205 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 205 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 205 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 205 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 205 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 205 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 205 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 205 " 0.005 2.00e-02 2.50e+03 ... (remaining 5152 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 521 2.70 - 3.25: 27573 3.25 - 3.80: 45385 3.80 - 4.35: 57573 4.35 - 4.90: 98580 Nonbonded interactions: 229632 Sorted by model distance: nonbonded pdb=" O ALA D 447 " pdb=" OG SER D 459 " model vdw 2.148 3.040 nonbonded pdb=" OH TYR C 5 " pdb=" OE2 GLU C 9 " model vdw 2.176 3.040 nonbonded pdb=" O GLY A 614 " pdb=" OG1 THR A 676 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR A 552 " pdb=" OE2 GLU A 678 " model vdw 2.202 3.040 nonbonded pdb=" O PRO C 391 " pdb=" ND2 ASN C 396 " model vdw 2.203 3.120 ... (remaining 229627 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 719) selection = (chain 'C' and resid 1 through 719) selection = (chain 'D' and resid 1 through 719) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 63.770 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.006 0.329 28442 Z= 0.283 Angle : 0.727 17.198 38618 Z= 0.402 Chirality : 0.041 0.326 4305 Planarity : 0.006 0.136 5155 Dihedral : 16.036 89.907 10665 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3585 helix: 1.66 (0.12), residues: 1828 sheet: -0.69 (0.23), residues: 477 loop : -0.26 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP B 205 HIS 0.004 0.001 HIS B 60 PHE 0.022 0.002 PHE C 352 TYR 0.029 0.002 TYR B 209 ARG 0.015 0.001 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.13032 ( 1588) hydrogen bonds : angle 6.04563 ( 4587) covalent geometry : bond 0.00576 (28442) covalent geometry : angle 0.72671 (38618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8084 (m90) cc_final: 0.7804 (m90) REVERT: A 370 LEU cc_start: 0.6170 (mm) cc_final: 0.5965 (mt) REVERT: A 554 ARG cc_start: 0.7287 (mtm110) cc_final: 0.7063 (mtp180) REVERT: A 606 VAL cc_start: 0.8948 (t) cc_final: 0.8748 (m) REVERT: B 57 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8451 (tp) REVERT: B 208 HIS cc_start: 0.7859 (t-170) cc_final: 0.7591 (t-170) REVERT: C 57 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8405 (tt) REVERT: C 657 ARG cc_start: 0.7858 (mmp80) cc_final: 0.7588 (mmp80) REVERT: D 208 HIS cc_start: 0.6341 (m90) cc_final: 0.6062 (m90) REVERT: E 1 MET cc_start: 0.5700 (ppp) cc_final: 0.5423 (ppp) REVERT: E 205 TRP cc_start: 0.8475 (m100) cc_final: 0.8217 (m100) REVERT: E 287 ARG cc_start: 0.6092 (mmt90) cc_final: 0.5390 (ptp90) REVERT: E 368 GLU cc_start: 0.7113 (mp0) cc_final: 0.6806 (mp0) outliers start: 4 outliers final: 1 residues processed: 215 average time/residue: 0.4245 time to fit residues: 142.3840 Evaluate side-chains 144 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 57 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 5.9990 chunk 269 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 278 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 322 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN C 332 ASN C 396 ASN C 543 HIS C 623 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.145947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.104245 restraints weight = 49475.014| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.56 r_work: 0.3185 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28442 Z= 0.144 Angle : 0.566 11.049 38618 Z= 0.283 Chirality : 0.039 0.191 4305 Planarity : 0.005 0.095 5155 Dihedral : 4.318 49.606 4006 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.46 % Rotamer: Outliers : 0.49 % Allowed : 4.97 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.14), residues: 3585 helix: 1.77 (0.12), residues: 1852 sheet: -0.81 (0.23), residues: 468 loop : -0.06 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 205 HIS 0.007 0.001 HIS D 560 PHE 0.015 0.001 PHE A 221 TYR 0.018 0.002 TYR B 209 ARG 0.007 0.000 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 1588) hydrogen bonds : angle 4.88885 ( 4587) covalent geometry : bond 0.00323 (28442) covalent geometry : angle 0.56602 (38618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8073 (m90) cc_final: 0.7824 (m90) REVERT: B 208 HIS cc_start: 0.8007 (t-170) cc_final: 0.7608 (t-170) REVERT: B 209 TYR cc_start: 0.7252 (t80) cc_final: 0.6438 (t80) REVERT: B 510 TYR cc_start: 0.8349 (m-10) cc_final: 0.8099 (m-10) REVERT: D 556 ARG cc_start: 0.7692 (tpp80) cc_final: 0.7191 (mmm160) REVERT: E 1 MET cc_start: 0.5598 (ppp) cc_final: 0.5348 (ppp) REVERT: E 205 TRP cc_start: 0.8535 (m100) cc_final: 0.8254 (m100) REVERT: E 287 ARG cc_start: 0.6227 (mmt90) cc_final: 0.5459 (ptp90) outliers start: 14 outliers final: 10 residues processed: 174 average time/residue: 0.3914 time to fit residues: 109.0632 Evaluate side-chains 152 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain E residue 558 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 233 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 272 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 335 optimal weight: 8.9990 chunk 72 optimal weight: 0.0970 chunk 241 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN ** C 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 679 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.143804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.103176 restraints weight = 49976.673| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.50 r_work: 0.3170 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28442 Z= 0.140 Angle : 0.531 11.840 38618 Z= 0.264 Chirality : 0.038 0.231 4305 Planarity : 0.005 0.089 5155 Dihedral : 4.217 52.733 4006 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 0.81 % Allowed : 6.67 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.14), residues: 3585 helix: 1.85 (0.12), residues: 1864 sheet: -0.72 (0.23), residues: 442 loop : -0.10 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 205 HIS 0.003 0.001 HIS E 303 PHE 0.016 0.001 PHE D 135 TYR 0.016 0.002 TYR B 50 ARG 0.008 0.000 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 1588) hydrogen bonds : angle 4.62402 ( 4587) covalent geometry : bond 0.00317 (28442) covalent geometry : angle 0.53138 (38618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.8661 (m-80) cc_final: 0.8027 (m-80) REVERT: A 208 HIS cc_start: 0.8123 (m90) cc_final: 0.7856 (m90) REVERT: A 250 TRP cc_start: 0.6289 (m100) cc_final: 0.5790 (m100) REVERT: B 209 TYR cc_start: 0.6974 (t80) cc_final: 0.6317 (t80) REVERT: B 510 TYR cc_start: 0.8340 (m-10) cc_final: 0.8127 (m-10) REVERT: C 205 TRP cc_start: 0.7554 (t-100) cc_final: 0.7311 (t-100) REVERT: C 657 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7404 (mmt90) REVERT: D 199 ARG cc_start: 0.7082 (mtm110) cc_final: 0.6849 (mtm110) REVERT: E 1 MET cc_start: 0.5569 (ppp) cc_final: 0.5330 (ppp) REVERT: E 205 TRP cc_start: 0.8513 (m100) cc_final: 0.8237 (m100) REVERT: E 287 ARG cc_start: 0.6234 (mmt90) cc_final: 0.5460 (ptp90) outliers start: 23 outliers final: 14 residues processed: 173 average time/residue: 0.4038 time to fit residues: 112.0735 Evaluate side-chains 160 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 500 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 261 optimal weight: 0.5980 chunk 294 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 253 optimal weight: 0.3980 chunk 217 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.143958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.103223 restraints weight = 50551.609| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.52 r_work: 0.3169 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28442 Z= 0.128 Angle : 0.518 14.583 38618 Z= 0.255 Chirality : 0.038 0.231 4305 Planarity : 0.004 0.087 5155 Dihedral : 4.117 53.627 4006 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.45 % Favored : 97.46 % Rotamer: Outliers : 0.99 % Allowed : 8.11 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.14), residues: 3585 helix: 1.97 (0.12), residues: 1857 sheet: -0.84 (0.23), residues: 464 loop : -0.02 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 205 HIS 0.006 0.001 HIS D 560 PHE 0.017 0.001 PHE A 221 TYR 0.016 0.001 TYR A 420 ARG 0.009 0.000 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 1588) hydrogen bonds : angle 4.44440 ( 4587) covalent geometry : bond 0.00289 (28442) covalent geometry : angle 0.51759 (38618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8175 (m90) cc_final: 0.7182 (t-170) REVERT: A 250 TRP cc_start: 0.6315 (m100) cc_final: 0.5836 (m100) REVERT: B 209 TYR cc_start: 0.7270 (t80) cc_final: 0.7053 (t80) REVERT: B 510 TYR cc_start: 0.8321 (m-10) cc_final: 0.8112 (m-10) REVERT: C 205 TRP cc_start: 0.7525 (t-100) cc_final: 0.7176 (t-100) REVERT: C 657 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7518 (mmt90) REVERT: C 678 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6965 (tt0) REVERT: D 207 LEU cc_start: 0.8463 (mt) cc_final: 0.8169 (tt) REVERT: E 1 MET cc_start: 0.5732 (ppp) cc_final: 0.5460 (ppp) REVERT: E 205 TRP cc_start: 0.8506 (m100) cc_final: 0.8225 (m100) REVERT: E 287 ARG cc_start: 0.6275 (mmt90) cc_final: 0.5484 (ptp90) REVERT: E 611 ASP cc_start: 0.7406 (t0) cc_final: 0.6879 (p0) outliers start: 28 outliers final: 17 residues processed: 186 average time/residue: 0.3974 time to fit residues: 118.8185 Evaluate side-chains 167 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 500 ASN Chi-restraints excluded: chain E residue 569 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 342 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 325 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 124 optimal weight: 0.6980 chunk 315 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 142 GLN B 60 HIS C 208 HIS E 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.141857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096735 restraints weight = 49962.869| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.21 r_work: 0.3094 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 28442 Z= 0.263 Angle : 0.611 11.874 38618 Z= 0.305 Chirality : 0.041 0.216 4305 Planarity : 0.005 0.071 5155 Dihedral : 4.350 58.309 4006 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 1.41 % Allowed : 9.35 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.14), residues: 3585 helix: 1.77 (0.12), residues: 1852 sheet: -0.98 (0.22), residues: 462 loop : -0.15 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 205 HIS 0.005 0.001 HIS D 543 PHE 0.017 0.002 PHE D 629 TYR 0.027 0.002 TYR B 50 ARG 0.008 0.001 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 1588) hydrogen bonds : angle 4.63733 ( 4587) covalent geometry : bond 0.00617 (28442) covalent geometry : angle 0.61132 (38618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8074 (m90) cc_final: 0.7817 (m90) REVERT: B 57 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8649 (tt) REVERT: B 209 TYR cc_start: 0.7481 (t80) cc_final: 0.7226 (t80) REVERT: B 254 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7773 (tp) REVERT: B 655 THR cc_start: 0.9157 (p) cc_final: 0.8871 (p) REVERT: C 477 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8205 (mm-30) REVERT: C 646 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8562 (pp) REVERT: C 657 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7736 (mmt90) REVERT: C 678 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7007 (tt0) REVERT: D 77 ASP cc_start: 0.7935 (m-30) cc_final: 0.7673 (m-30) REVERT: D 207 LEU cc_start: 0.8545 (mt) cc_final: 0.8238 (tt) REVERT: D 298 ARG cc_start: 0.8870 (mtp180) cc_final: 0.8649 (mtm-85) REVERT: E 1 MET cc_start: 0.5693 (ppp) cc_final: 0.5412 (ppp) REVERT: E 287 ARG cc_start: 0.6350 (mmt90) cc_final: 0.5482 (ptp90) outliers start: 40 outliers final: 22 residues processed: 192 average time/residue: 0.4216 time to fit residues: 130.0909 Evaluate side-chains 172 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 569 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 190 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 241 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 175 optimal weight: 0.0040 chunk 27 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 9.9990 chunk 317 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.144557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.101269 restraints weight = 50111.448| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.30 r_work: 0.3168 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28442 Z= 0.106 Angle : 0.515 14.186 38618 Z= 0.252 Chirality : 0.037 0.207 4305 Planarity : 0.004 0.065 5155 Dihedral : 4.127 55.088 4006 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.34 % Favored : 97.57 % Rotamer: Outliers : 1.06 % Allowed : 10.41 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.14), residues: 3585 helix: 1.95 (0.12), residues: 1861 sheet: -0.89 (0.23), residues: 465 loop : -0.07 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 205 HIS 0.004 0.001 HIS D 560 PHE 0.017 0.001 PHE A 47 TYR 0.016 0.001 TYR B 557 ARG 0.012 0.000 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 1588) hydrogen bonds : angle 4.37891 ( 4587) covalent geometry : bond 0.00228 (28442) covalent geometry : angle 0.51492 (38618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.8632 (pmm) cc_final: 0.7677 (pmm) REVERT: A 706 PHE cc_start: 0.7439 (m-10) cc_final: 0.7112 (m-10) REVERT: C 1 MET cc_start: 0.6637 (tpt) cc_final: 0.6322 (mmm) REVERT: C 646 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8555 (pp) REVERT: C 657 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7666 (mmt90) REVERT: C 678 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6927 (tt0) REVERT: D 207 LEU cc_start: 0.8468 (mt) cc_final: 0.8196 (tt) REVERT: D 208 HIS cc_start: 0.6654 (m90) cc_final: 0.6181 (m90) REVERT: D 298 ARG cc_start: 0.8726 (mtp180) cc_final: 0.8517 (mtm-85) REVERT: D 646 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8634 (pp) REVERT: E 1 MET cc_start: 0.5482 (ppp) cc_final: 0.5209 (ppp) REVERT: E 287 ARG cc_start: 0.6351 (mmt90) cc_final: 0.5482 (ptp90) REVERT: E 611 ASP cc_start: 0.7429 (t0) cc_final: 0.6806 (p0) outliers start: 30 outliers final: 17 residues processed: 200 average time/residue: 0.3824 time to fit residues: 123.2373 Evaluate side-chains 176 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 510 TYR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 500 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 352 optimal weight: 0.0970 chunk 282 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 332 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.143061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.098369 restraints weight = 49801.524| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.34 r_work: 0.3135 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28442 Z= 0.147 Angle : 0.526 11.729 38618 Z= 0.259 Chirality : 0.038 0.207 4305 Planarity : 0.004 0.057 5155 Dihedral : 4.102 56.746 4006 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 1.27 % Allowed : 10.65 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.14), residues: 3585 helix: 1.97 (0.12), residues: 1862 sheet: -0.86 (0.23), residues: 464 loop : -0.05 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 10 HIS 0.004 0.001 HIS D 560 PHE 0.017 0.001 PHE B 571 TYR 0.017 0.001 TYR B 50 ARG 0.006 0.000 ARG A 688 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 1588) hydrogen bonds : angle 4.36287 ( 4587) covalent geometry : bond 0.00339 (28442) covalent geometry : angle 0.52634 (38618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8202 (m90) cc_final: 0.7376 (t-170) REVERT: A 356 MET cc_start: 0.8706 (pmm) cc_final: 0.7687 (pmm) REVERT: A 688 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7867 (mmm-85) REVERT: B 57 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8642 (tt) REVERT: C 1 MET cc_start: 0.6596 (tpt) cc_final: 0.6279 (mmm) REVERT: C 646 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8535 (pp) REVERT: C 657 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7695 (mmt90) REVERT: C 678 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6989 (tt0) REVERT: D 126 ARG cc_start: 0.7963 (ptm160) cc_final: 0.7601 (ptm160) REVERT: D 207 LEU cc_start: 0.8499 (mt) cc_final: 0.8215 (tt) REVERT: D 208 HIS cc_start: 0.6696 (m90) cc_final: 0.6163 (m90) REVERT: D 298 ARG cc_start: 0.8805 (mtp180) cc_final: 0.8586 (mtm-85) REVERT: D 646 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8618 (pp) REVERT: E 1 MET cc_start: 0.5457 (ppp) cc_final: 0.5206 (ppp) REVERT: E 287 ARG cc_start: 0.6416 (mmt90) cc_final: 0.5526 (ptp90) REVERT: E 611 ASP cc_start: 0.7375 (t0) cc_final: 0.6691 (p0) outliers start: 36 outliers final: 21 residues processed: 188 average time/residue: 0.4103 time to fit residues: 125.1911 Evaluate side-chains 178 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain E residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 18 optimal weight: 40.0000 chunk 285 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 574 ASN ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.143296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.099215 restraints weight = 50256.189| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.44 r_work: 0.3135 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28442 Z= 0.144 Angle : 0.531 14.026 38618 Z= 0.259 Chirality : 0.038 0.233 4305 Planarity : 0.004 0.068 5155 Dihedral : 4.084 56.879 4006 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 1.20 % Allowed : 11.39 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), residues: 3585 helix: 1.99 (0.12), residues: 1865 sheet: -0.85 (0.23), residues: 454 loop : -0.09 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 10 HIS 0.003 0.001 HIS D 543 PHE 0.029 0.001 PHE B 571 TYR 0.017 0.001 TYR B 50 ARG 0.015 0.000 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 1588) hydrogen bonds : angle 4.33519 ( 4587) covalent geometry : bond 0.00330 (28442) covalent geometry : angle 0.53114 (38618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8227 (m90) cc_final: 0.7457 (t-170) REVERT: A 356 MET cc_start: 0.8741 (pmm) cc_final: 0.7774 (pmm) REVERT: A 688 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7839 (mmm-85) REVERT: B 57 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8679 (tt) REVERT: C 1 MET cc_start: 0.6594 (tpt) cc_final: 0.6278 (mmm) REVERT: C 646 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8540 (pp) REVERT: C 657 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7697 (mmt90) REVERT: C 678 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6959 (tt0) REVERT: D 207 LEU cc_start: 0.8513 (mt) cc_final: 0.8227 (tt) REVERT: D 208 HIS cc_start: 0.6712 (m90) cc_final: 0.6182 (m90) REVERT: D 556 ARG cc_start: 0.7649 (tpp80) cc_final: 0.7244 (mmm160) REVERT: D 646 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8633 (pp) REVERT: E 1 MET cc_start: 0.5602 (ppp) cc_final: 0.5349 (ppp) REVERT: E 287 ARG cc_start: 0.6445 (mmt90) cc_final: 0.5534 (ptp90) REVERT: E 611 ASP cc_start: 0.7385 (t0) cc_final: 0.6681 (p0) outliers start: 34 outliers final: 25 residues processed: 188 average time/residue: 0.3887 time to fit residues: 117.4452 Evaluate side-chains 186 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 411 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 139 optimal weight: 0.0470 chunk 295 optimal weight: 4.9990 chunk 299 optimal weight: 8.9990 chunk 263 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 307 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.142868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098488 restraints weight = 50149.455| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.45 r_work: 0.3121 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28442 Z= 0.154 Angle : 0.534 12.046 38618 Z= 0.260 Chirality : 0.038 0.236 4305 Planarity : 0.004 0.053 5155 Dihedral : 4.089 57.017 4006 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 1.20 % Allowed : 11.68 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.14), residues: 3585 helix: 2.01 (0.12), residues: 1861 sheet: -0.86 (0.23), residues: 455 loop : -0.08 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 10 HIS 0.003 0.001 HIS D 543 PHE 0.022 0.001 PHE B 571 TYR 0.017 0.001 TYR B 50 ARG 0.007 0.000 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 1588) hydrogen bonds : angle 4.34212 ( 4587) covalent geometry : bond 0.00357 (28442) covalent geometry : angle 0.53358 (38618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8227 (m90) cc_final: 0.7444 (t-170) REVERT: A 356 MET cc_start: 0.8737 (pmm) cc_final: 0.7775 (pmm) REVERT: B 57 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8684 (tt) REVERT: C 134 ARG cc_start: 0.7303 (ptm-80) cc_final: 0.7060 (tmm160) REVERT: C 646 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8551 (pp) REVERT: C 657 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7703 (mmt90) REVERT: C 678 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6846 (tt0) REVERT: D 77 ASP cc_start: 0.7838 (m-30) cc_final: 0.7580 (m-30) REVERT: D 207 LEU cc_start: 0.8512 (mt) cc_final: 0.8236 (tt) REVERT: D 208 HIS cc_start: 0.6762 (m90) cc_final: 0.6219 (m90) REVERT: D 556 ARG cc_start: 0.7646 (tpp80) cc_final: 0.7251 (mmm160) REVERT: D 646 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8640 (pp) REVERT: E 1 MET cc_start: 0.5566 (ppp) cc_final: 0.5306 (ppp) REVERT: E 287 ARG cc_start: 0.6462 (mmt90) cc_final: 0.5528 (ptp90) REVERT: E 611 ASP cc_start: 0.7402 (t0) cc_final: 0.6708 (p0) outliers start: 34 outliers final: 24 residues processed: 184 average time/residue: 0.3940 time to fit residues: 116.3129 Evaluate side-chains 183 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain E residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 248 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 296 optimal weight: 20.0000 chunk 217 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 288 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 574 ASN ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.142601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.098269 restraints weight = 49772.515| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.27 r_work: 0.3122 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28442 Z= 0.150 Angle : 0.539 13.503 38618 Z= 0.263 Chirality : 0.038 0.232 4305 Planarity : 0.004 0.074 5155 Dihedral : 4.092 56.731 4006 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.06 % Allowed : 12.06 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.14), residues: 3585 helix: 2.03 (0.12), residues: 1860 sheet: -0.84 (0.23), residues: 453 loop : -0.08 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 10 HIS 0.003 0.001 HIS D 543 PHE 0.023 0.001 PHE B 571 TYR 0.017 0.001 TYR B 50 ARG 0.017 0.000 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 1588) hydrogen bonds : angle 4.32548 ( 4587) covalent geometry : bond 0.00347 (28442) covalent geometry : angle 0.53948 (38618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 TRP cc_start: 0.6162 (m100) cc_final: 0.5900 (m100) REVERT: A 356 MET cc_start: 0.8754 (pmm) cc_final: 0.7816 (pmm) REVERT: B 57 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8693 (tt) REVERT: B 529 ILE cc_start: 0.8481 (mt) cc_final: 0.7979 (pt) REVERT: C 134 ARG cc_start: 0.7478 (ptm-80) cc_final: 0.7202 (tmm160) REVERT: C 646 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8556 (pp) REVERT: C 657 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7707 (mmt90) REVERT: C 678 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6977 (tt0) REVERT: C 689 MET cc_start: 0.6136 (mmm) cc_final: 0.5806 (mmm) REVERT: D 77 ASP cc_start: 0.7828 (m-30) cc_final: 0.7428 (m-30) REVERT: D 207 LEU cc_start: 0.8545 (mt) cc_final: 0.8260 (tt) REVERT: D 208 HIS cc_start: 0.6778 (m90) cc_final: 0.6249 (m90) REVERT: D 556 ARG cc_start: 0.7639 (tpp80) cc_final: 0.7237 (mmm160) REVERT: D 646 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8639 (pp) REVERT: E 1 MET cc_start: 0.5648 (ppp) cc_final: 0.5381 (ppp) REVERT: E 287 ARG cc_start: 0.6475 (mmt90) cc_final: 0.5508 (ptp90) REVERT: E 611 ASP cc_start: 0.7425 (t0) cc_final: 0.6739 (p0) outliers start: 30 outliers final: 24 residues processed: 181 average time/residue: 0.3972 time to fit residues: 116.7720 Evaluate side-chains 184 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain E residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 305 optimal weight: 6.9990 chunk 73 optimal weight: 0.1980 chunk 151 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 623 ASN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.143665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.099631 restraints weight = 50094.506| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.14 r_work: 0.3157 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28442 Z= 0.114 Angle : 0.521 12.343 38618 Z= 0.253 Chirality : 0.038 0.283 4305 Planarity : 0.004 0.054 5155 Dihedral : 4.053 55.945 4006 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 0.92 % Allowed : 11.99 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.14), residues: 3585 helix: 2.07 (0.12), residues: 1860 sheet: -0.81 (0.23), residues: 453 loop : -0.06 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 10 HIS 0.003 0.001 HIS D 543 PHE 0.022 0.001 PHE B 571 TYR 0.015 0.001 TYR A 420 ARG 0.008 0.000 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 1588) hydrogen bonds : angle 4.29101 ( 4587) covalent geometry : bond 0.00256 (28442) covalent geometry : angle 0.52114 (38618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13798.74 seconds wall clock time: 238 minutes 55.43 seconds (14335.43 seconds total)