Starting phenix.real_space_refine on Thu Dec 26 15:00:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6k_42994/12_2024/8v6k_42994_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6k_42994/12_2024/8v6k_42994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v6k_42994/12_2024/8v6k_42994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6k_42994/12_2024/8v6k_42994.map" model { file = "/net/cci-nas-00/data/ceres_data/8v6k_42994/12_2024/8v6k_42994_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6k_42994/12_2024/8v6k_42994_trim.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 32 5.49 5 S 128 5.16 5 Na 4 4.78 5 C 14888 2.51 5 N 3488 2.21 5 O 4341 1.98 5 H 21100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 43981 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10484 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "B" Number of atoms: 10484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10484 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "C" Number of atoms: 10484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10484 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "D" Number of atoms: 10484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10484 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "A" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 418 Unusual residues: {' NA': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 418 Unusual residues: {' NA': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "C" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Time building chain proxies: 19.48, per 1000 atoms: 0.44 Number of scatterers: 43981 At special positions: 0 Unit cell: (153.6, 152.8, 131.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 128 16.00 P 32 15.00 Na 4 11.00 O 4341 8.00 N 3488 7.00 C 14888 6.00 H 21100 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.04 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.04 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.04 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.04 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: 12.27 Conformation dependent library (CDL) restraints added in 3.1 seconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 66.4% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.101A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 149 removed outlier: 3.676A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.668A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.542A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.611A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.577A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.632A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.566A pdb=" N GLU A 467 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 469 " --> pdb=" O GLU A 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 464 through 469' Processing helix chain 'A' and resid 482 through 509 removed outlier: 4.025A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 520 removed outlier: 4.593A pdb=" N ILE A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 543 removed outlier: 3.580A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.625A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.890A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 removed outlier: 3.507A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.531A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.529A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 removed outlier: 3.695A pdb=" N ARG A 714 " --> pdb=" O TRP A 710 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 4.100A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 149 removed outlier: 3.675A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 removed outlier: 3.668A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.543A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.612A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.577A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.632A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.567A pdb=" N GLU B 467 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 468 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 469 " --> pdb=" O GLU B 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 464 through 469' Processing helix chain 'B' and resid 482 through 509 removed outlier: 4.025A pdb=" N ARG B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 520 removed outlier: 4.593A pdb=" N ILE B 516 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 543 removed outlier: 3.580A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.625A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.890A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 removed outlier: 3.506A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.531A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.529A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 removed outlier: 3.695A pdb=" N ARG B 714 " --> pdb=" O TRP B 710 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 4.100A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 149 removed outlier: 3.676A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 removed outlier: 3.668A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.543A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.612A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.577A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.632A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 464 through 469 removed outlier: 3.567A pdb=" N GLU C 467 " --> pdb=" O ARG C 464 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 468 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C 469 " --> pdb=" O GLU C 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 464 through 469' Processing helix chain 'C' and resid 482 through 509 removed outlier: 4.025A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 509 " --> pdb=" O ILE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 520 removed outlier: 4.592A pdb=" N ILE C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 543 removed outlier: 3.580A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.625A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.890A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 removed outlier: 3.506A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 686 removed outlier: 3.531A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.529A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 removed outlier: 3.695A pdb=" N ARG C 714 " --> pdb=" O TRP C 710 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 4.100A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 126 " --> pdb=" O ARG D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 149 removed outlier: 3.676A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 162 removed outlier: 3.668A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.543A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.611A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.577A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 410 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.632A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.568A pdb=" N GLU D 467 " --> pdb=" O ARG D 464 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 468 " --> pdb=" O GLU D 465 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE D 469 " --> pdb=" O GLU D 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 464 through 469' Processing helix chain 'D' and resid 482 through 509 removed outlier: 4.025A pdb=" N ARG D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG D 509 " --> pdb=" O ILE D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 520 removed outlier: 4.592A pdb=" N ILE D 516 " --> pdb=" O ASP D 512 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 543 removed outlier: 3.580A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.624A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.890A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 removed outlier: 3.507A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 686 removed outlier: 3.531A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.529A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 removed outlier: 3.696A pdb=" N ARG D 714 " --> pdb=" O TRP D 710 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.823A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.823A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.823A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.821A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 3228 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: 16.09 Time building geometry restraints manager: 14.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 21064 1.03 - 1.23: 114 1.23 - 1.42: 9006 1.42 - 1.62: 13636 1.62 - 1.82: 212 Bond restraints: 44032 Sorted by residual: bond pdb=" O12 POV B 902 " pdb=" P POV B 902 " ideal model delta sigma weight residual 1.657 1.593 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O12 POV C 902 " pdb=" P POV C 902 " ideal model delta sigma weight residual 1.657 1.593 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O12 POV A 908 " pdb=" P POV A 908 " ideal model delta sigma weight residual 1.657 1.593 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O12 POV B 904 " pdb=" P POV B 904 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O12 POV D 904 " pdb=" P POV D 904 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 9.93e+00 ... (remaining 44027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.60: 78463 5.60 - 11.20: 116 11.20 - 16.81: 5 16.81 - 22.41: 4 22.41 - 28.01: 8 Bond angle restraints: 78596 Sorted by residual: angle pdb=" CG2 VAL B 596 " pdb=" CB VAL B 596 " pdb=" HB VAL B 596 " ideal model delta sigma weight residual 108.00 79.99 28.01 3.00e+00 1.11e-01 8.72e+01 angle pdb=" CG2 VAL A 596 " pdb=" CB VAL A 596 " pdb=" HB VAL A 596 " ideal model delta sigma weight residual 108.00 80.02 27.98 3.00e+00 1.11e-01 8.70e+01 angle pdb=" CG2 VAL C 596 " pdb=" CB VAL C 596 " pdb=" HB VAL C 596 " ideal model delta sigma weight residual 108.00 80.08 27.92 3.00e+00 1.11e-01 8.66e+01 angle pdb=" CG2 VAL D 596 " pdb=" CB VAL D 596 " pdb=" HB VAL D 596 " ideal model delta sigma weight residual 108.00 80.09 27.91 3.00e+00 1.11e-01 8.66e+01 angle pdb=" CG1 VAL D 596 " pdb=" CB VAL D 596 " pdb=" HB VAL D 596 " ideal model delta sigma weight residual 108.00 82.75 25.25 3.00e+00 1.11e-01 7.08e+01 ... (remaining 78591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 20458 35.72 - 71.44: 576 71.44 - 107.16: 62 107.16 - 142.88: 37 142.88 - 178.60: 27 Dihedral angle restraints: 21160 sinusoidal: 12004 harmonic: 9156 Sorted by residual: dihedral pdb=" CA HIS A 477 " pdb=" C HIS A 477 " pdb=" N LYS A 478 " pdb=" CA LYS A 478 " ideal model delta harmonic sigma weight residual -180.00 -129.01 -50.99 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA HIS D 477 " pdb=" C HIS D 477 " pdb=" N LYS D 478 " pdb=" CA LYS D 478 " ideal model delta harmonic sigma weight residual -180.00 -129.02 -50.98 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA HIS B 477 " pdb=" C HIS B 477 " pdb=" N LYS B 478 " pdb=" CA LYS B 478 " ideal model delta harmonic sigma weight residual -180.00 -129.02 -50.98 0 5.00e+00 4.00e-02 1.04e+02 ... (remaining 21157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.345: 3304 0.345 - 0.691: 0 0.691 - 1.036: 0 1.036 - 1.382: 0 1.382 - 1.727: 4 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CB VAL A 596 " pdb=" CA VAL A 596 " pdb=" CG1 VAL A 596 " pdb=" CG2 VAL A 596 " both_signs ideal model delta sigma weight residual False -2.63 -0.90 -1.73 2.00e-01 2.50e+01 7.46e+01 chirality pdb=" CB VAL D 596 " pdb=" CA VAL D 596 " pdb=" CG1 VAL D 596 " pdb=" CG2 VAL D 596 " both_signs ideal model delta sigma weight residual False -2.63 -0.90 -1.73 2.00e-01 2.50e+01 7.45e+01 chirality pdb=" CB VAL C 596 " pdb=" CA VAL C 596 " pdb=" CG1 VAL C 596 " pdb=" CG2 VAL C 596 " both_signs ideal model delta sigma weight residual False -2.63 -0.90 -1.73 2.00e-01 2.50e+01 7.45e+01 ... (remaining 3305 not shown) Planarity restraints: 6188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 220 " -0.099 2.00e-02 2.50e+03 1.06e-01 1.68e+02 pdb=" CG ASN B 220 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 220 " 0.088 2.00e-02 2.50e+03 pdb=" ND2 ASN B 220 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 220 " 0.150 2.00e-02 2.50e+03 pdb="HD22 ASN B 220 " -0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 220 " 0.099 2.00e-02 2.50e+03 1.05e-01 1.65e+02 pdb=" CG ASN D 220 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN D 220 " -0.087 2.00e-02 2.50e+03 pdb=" ND2 ASN D 220 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN D 220 " -0.149 2.00e-02 2.50e+03 pdb="HD22 ASN D 220 " 0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 220 " 0.098 2.00e-02 2.50e+03 1.04e-01 1.62e+02 pdb=" CG ASN C 220 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 220 " -0.086 2.00e-02 2.50e+03 pdb=" ND2 ASN C 220 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 220 " -0.148 2.00e-02 2.50e+03 pdb="HD22 ASN C 220 " 0.160 2.00e-02 2.50e+03 ... (remaining 6185 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 3349 2.25 - 2.84: 97428 2.84 - 3.42: 110881 3.42 - 4.01: 156576 4.01 - 4.60: 241987 Nonbonded interactions: 610221 Sorted by model distance: nonbonded pdb=" OE1 GLU B 224 " pdb="HH11 ARG B 225 " model vdw 1.658 2.450 nonbonded pdb=" OE1 GLU D 224 " pdb="HH11 ARG D 225 " model vdw 1.659 2.450 nonbonded pdb=" OE1 GLU C 224 " pdb="HH11 ARG C 225 " model vdw 1.660 2.450 nonbonded pdb=" OE1 GLU A 224 " pdb="HH11 ARG A 225 " model vdw 1.660 2.450 nonbonded pdb=" O ARG A 118 " pdb="HH21 ARG A 122 " model vdw 1.670 2.450 ... (remaining 610216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 117 through 756 or resid 901 through 908)) selection = (chain 'B' and (resid 117 through 756 or resid 901 through 908)) selection = chain 'C' selection = chain 'D' } 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=0.45 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: 0.890 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: 0.810 Extract box with map and model: 1.950 Check model and map are aligned: 0.330 Set scattering table: 0.430 Process input model: 84.410 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.160 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:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 0.064 22932 Z= 0.394 Angle : 0.998 12.006 30712 Z= 0.491 Chirality : 0.073 1.727 3308 Planarity : 0.004 0.040 3700 Dihedral : 19.804 178.604 9200 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.54 % Favored : 92.67 % Rotamer: Outliers : 0.18 % Allowed : 3.00 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.78 (0.14), residues: 2552 helix: -2.22 (0.10), residues: 1504 sheet: -0.46 (0.43), residues: 68 loop : -2.96 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 739 HIS 0.029 0.002 HIS A 256 PHE 0.015 0.001 PHE D 316 TYR 0.015 0.002 TYR D 650 ARG 0.009 0.001 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 456 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 562 MET cc_start: 0.7426 (mmm) cc_final: 0.6728 (mmt) REVERT: C 562 MET cc_start: 0.7450 (mmm) cc_final: 0.6179 (mmt) REVERT: D 562 MET cc_start: 0.7087 (mmm) cc_final: 0.6177 (mmt) outliers start: 4 outliers final: 3 residues processed: 460 average time/residue: 3.1028 time to fit residues: 1626.3606 Evaluate side-chains 211 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 208 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 503 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 417 HIS A 471 HIS A 523 HIS B 220 ASN B 227 GLN B 394 ASN B 645 GLN C 220 ASN C 227 GLN C 417 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS D 220 ASN D 227 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22932 Z= 0.274 Angle : 0.696 12.167 30712 Z= 0.359 Chirality : 0.070 1.716 3308 Planarity : 0.005 0.086 3700 Dihedral : 23.341 179.442 4166 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.94 % Favored : 92.59 % Rotamer: Outliers : 2.07 % Allowed : 9.61 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.16), residues: 2552 helix: 0.52 (0.13), residues: 1548 sheet: 0.60 (0.46), residues: 84 loop : -2.95 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 692 HIS 0.016 0.002 HIS D 256 PHE 0.023 0.002 PHE B 542 TYR 0.015 0.002 TYR D 575 ARG 0.008 0.001 ARG D 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 3.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 682 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: D 563 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7645 (mm) outliers start: 47 outliers final: 7 residues processed: 249 average time/residue: 2.9894 time to fit residues: 852.3421 Evaluate side-chains 172 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 696 ARG Chi-restraints excluded: chain D residue 721 CYS Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN B 412 ASN C 279 GLN C 394 ASN C 412 ASN D 394 ASN D 412 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 22932 Z= 0.301 Angle : 0.665 11.206 30712 Z= 0.346 Chirality : 0.070 1.682 3308 Planarity : 0.005 0.092 3700 Dihedral : 22.343 179.268 4160 Min Nonbonded Distance : 1.318 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.09 % Favored : 92.40 % Rotamer: Outliers : 1.85 % Allowed : 10.58 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.22 (0.16), residues: 2552 helix: 1.22 (0.13), residues: 1560 sheet: 1.42 (0.55), residues: 88 loop : -2.93 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 692 HIS 0.011 0.002 HIS C 256 PHE 0.028 0.002 PHE D 542 TYR 0.014 0.002 TYR A 451 ARG 0.011 0.001 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8529 (ttm) cc_final: 0.8322 (ttm) REVERT: A 418 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: A 581 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8421 (mptm) REVERT: D 195 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: D 419 MET cc_start: 0.8822 (mtp) cc_final: 0.8573 (mtp) REVERT: D 696 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8578 (ttt180) outliers start: 42 outliers final: 8 residues processed: 218 average time/residue: 2.9415 time to fit residues: 739.4385 Evaluate side-chains 162 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 696 ARG Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 647 ASN C 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 22932 Z= 0.323 Angle : 0.660 11.415 30712 Z= 0.344 Chirality : 0.071 1.719 3308 Planarity : 0.005 0.116 3700 Dihedral : 21.586 175.772 4160 Min Nonbonded Distance : 1.267 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.90 % Favored : 92.63 % Rotamer: Outliers : 1.90 % Allowed : 11.77 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.02 (0.17), residues: 2552 helix: 1.34 (0.13), residues: 1568 sheet: 0.86 (0.49), residues: 112 loop : -2.71 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 692 HIS 0.007 0.002 HIS A 256 PHE 0.016 0.002 PHE D 316 TYR 0.014 0.002 TYR B 451 ARG 0.010 0.001 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8546 (ttm) cc_final: 0.8338 (ttm) REVERT: A 581 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8480 (mptm) REVERT: B 188 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7419 (mtm-85) REVERT: B 696 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7555 (ttm-80) REVERT: B 716 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7981 (ttm-80) REVERT: D 195 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7352 (tp30) REVERT: D 479 MET cc_start: 0.3702 (ttt) cc_final: 0.3500 (ttm) REVERT: D 696 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8547 (ttt180) outliers start: 43 outliers final: 12 residues processed: 195 average time/residue: 2.9390 time to fit residues: 660.6440 Evaluate side-chains 163 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 696 ARG Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 696 ARG Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 211 optimal weight: 0.5980 chunk 171 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN B 647 ASN C 279 GLN C 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22932 Z= 0.237 Angle : 0.591 11.217 30712 Z= 0.309 Chirality : 0.067 1.644 3308 Planarity : 0.004 0.082 3700 Dihedral : 20.465 175.817 4160 Min Nonbonded Distance : 1.376 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.47 % Favored : 93.06 % Rotamer: Outliers : 1.63 % Allowed : 12.30 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.43 (0.17), residues: 2552 helix: 1.70 (0.13), residues: 1552 sheet: 0.96 (0.49), residues: 112 loop : -2.56 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 692 HIS 0.008 0.002 HIS A 256 PHE 0.011 0.001 PHE C 590 TYR 0.014 0.002 TYR B 451 ARG 0.004 0.000 ARG D 696 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7994 (tpp80) cc_final: 0.7499 (mtm-85) REVERT: A 256 HIS cc_start: 0.6552 (OUTLIER) cc_final: 0.5900 (m-70) REVERT: A 323 MET cc_start: 0.8530 (ttm) cc_final: 0.8327 (ttm) REVERT: A 581 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8453 (mptm) REVERT: A 716 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.8005 (ttm-80) REVERT: B 188 ARG cc_start: 0.7943 (tpp80) cc_final: 0.7443 (mtm-85) REVERT: B 256 HIS cc_start: 0.6417 (OUTLIER) cc_final: 0.5935 (m-70) REVERT: B 418 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: B 696 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7536 (ttm-80) REVERT: B 716 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7985 (ttm-80) REVERT: C 188 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7362 (mtm-85) REVERT: C 256 HIS cc_start: 0.6536 (OUTLIER) cc_final: 0.5917 (m-70) REVERT: C 418 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: C 488 MET cc_start: 0.7871 (mtp) cc_final: 0.7538 (mtm) REVERT: D 188 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7326 (mtm-85) REVERT: D 256 HIS cc_start: 0.6506 (OUTLIER) cc_final: 0.5882 (m-70) REVERT: D 418 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: D 479 MET cc_start: 0.3663 (ttt) cc_final: 0.3454 (ttm) REVERT: D 488 MET cc_start: 0.8000 (mtp) cc_final: 0.7682 (mtm) outliers start: 37 outliers final: 9 residues processed: 186 average time/residue: 2.9924 time to fit residues: 641.5185 Evaluate side-chains 170 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 3.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 696 ARG Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain D residue 256 HIS Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 721 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN C 279 GLN C 647 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22932 Z= 0.385 Angle : 0.686 11.385 30712 Z= 0.356 Chirality : 0.074 1.773 3308 Planarity : 0.005 0.129 3700 Dihedral : 21.202 179.983 4160 Min Nonbonded Distance : 1.269 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.05 % Favored : 92.48 % Rotamer: Outliers : 1.85 % Allowed : 12.43 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.11 (0.17), residues: 2552 helix: 1.32 (0.13), residues: 1580 sheet: 1.00 (0.50), residues: 112 loop : -2.54 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 692 HIS 0.006 0.002 HIS B 471 PHE 0.016 0.002 PHE D 316 TYR 0.017 0.002 TYR A 451 ARG 0.005 0.001 ARG A 696 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7989 (tpp80) cc_final: 0.7525 (mtm-85) REVERT: A 418 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: A 581 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8480 (mptm) REVERT: A 716 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8012 (ttm-80) REVERT: B 188 ARG cc_start: 0.7961 (tpp80) cc_final: 0.7479 (mtm-85) REVERT: B 256 HIS cc_start: 0.6789 (OUTLIER) cc_final: 0.5908 (m-70) REVERT: B 418 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: B 488 MET cc_start: 0.7964 (mtp) cc_final: 0.7683 (mtm) REVERT: B 696 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7498 (ttm-80) REVERT: B 716 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8002 (ttm-80) REVERT: C 188 ARG cc_start: 0.8045 (tpp80) cc_final: 0.7419 (mtm-85) REVERT: C 256 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.5863 (m-70) REVERT: C 418 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: C 581 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8511 (mptm) REVERT: D 188 ARG cc_start: 0.8002 (tpp80) cc_final: 0.7368 (mtm-85) REVERT: D 195 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7445 (tp30) REVERT: D 418 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: D 479 MET cc_start: 0.3868 (OUTLIER) cc_final: 0.3650 (ttm) REVERT: D 488 MET cc_start: 0.7978 (mtp) cc_final: 0.7708 (mtm) REVERT: D 716 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8032 (ttm-80) outliers start: 42 outliers final: 9 residues processed: 188 average time/residue: 3.3483 time to fit residues: 714.1002 Evaluate side-chains 173 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 696 ARG Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 581 LYS Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 721 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 246 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 279 GLN A 412 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN D 251 ASN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22932 Z= 0.178 Angle : 0.554 11.113 30712 Z= 0.291 Chirality : 0.065 1.592 3308 Planarity : 0.003 0.056 3700 Dihedral : 19.499 176.466 4160 Min Nonbonded Distance : 1.418 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.11 % Favored : 93.42 % Rotamer: Outliers : 1.06 % Allowed : 13.49 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.67 (0.17), residues: 2552 helix: 1.88 (0.13), residues: 1556 sheet: 0.98 (0.50), residues: 112 loop : -2.43 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 692 HIS 0.021 0.001 HIS A 256 PHE 0.010 0.001 PHE B 449 TYR 0.014 0.001 TYR B 451 ARG 0.003 0.000 ARG C 462 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7560 (mtm-85) REVERT: A 418 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: A 581 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8506 (mptm) REVERT: A 696 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8034 (ttt180) REVERT: A 716 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8005 (ttm-80) REVERT: B 188 ARG cc_start: 0.7983 (tpp80) cc_final: 0.7511 (mtm-85) REVERT: B 256 HIS cc_start: 0.6634 (OUTLIER) cc_final: 0.5868 (m-70) REVERT: B 418 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: B 716 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8000 (ttm-80) REVERT: C 188 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7435 (mtm-85) REVERT: C 256 HIS cc_start: 0.6729 (OUTLIER) cc_final: 0.5865 (m-70) REVERT: C 716 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7436 (ttm-80) REVERT: D 188 ARG cc_start: 0.7981 (tpp80) cc_final: 0.7373 (mtm-85) REVERT: D 418 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7074 (mp0) outliers start: 24 outliers final: 5 residues processed: 180 average time/residue: 3.1119 time to fit residues: 641.3056 Evaluate side-chains 168 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 721 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 286 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22932 Z= 0.258 Angle : 0.600 11.238 30712 Z= 0.313 Chirality : 0.068 1.667 3308 Planarity : 0.004 0.090 3700 Dihedral : 19.911 178.110 4160 Min Nonbonded Distance : 1.332 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.86 % Favored : 92.67 % Rotamer: Outliers : 1.32 % Allowed : 13.58 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2552 helix: 1.78 (0.13), residues: 1564 sheet: 0.92 (0.50), residues: 112 loop : -2.33 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 692 HIS 0.017 0.002 HIS A 256 PHE 0.013 0.001 PHE A 316 TYR 0.016 0.002 TYR B 451 ARG 0.005 0.000 ARG D 696 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8015 (tpp80) cc_final: 0.7555 (mtm-85) REVERT: A 418 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: A 581 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8459 (mptm) REVERT: A 716 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8002 (ttm-80) REVERT: B 188 ARG cc_start: 0.7983 (tpp80) cc_final: 0.7503 (mtm-85) REVERT: B 256 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.5860 (m-70) REVERT: B 716 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8005 (ttm-80) REVERT: C 188 ARG cc_start: 0.8037 (tpp80) cc_final: 0.7448 (mtm-85) REVERT: C 256 HIS cc_start: 0.6845 (OUTLIER) cc_final: 0.5787 (m-70) REVERT: C 716 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7445 (ttm-80) REVERT: D 188 ARG cc_start: 0.8000 (tpp80) cc_final: 0.7385 (mtm-85) outliers start: 30 outliers final: 7 residues processed: 177 average time/residue: 3.2073 time to fit residues: 646.0892 Evaluate side-chains 161 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 721 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 229 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 100 optimal weight: 0.0570 chunk 180 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22932 Z= 0.251 Angle : 0.591 11.248 30712 Z= 0.309 Chirality : 0.068 1.660 3308 Planarity : 0.004 0.078 3700 Dihedral : 19.715 178.040 4160 Min Nonbonded Distance : 1.341 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.31 % Favored : 93.22 % Rotamer: Outliers : 0.84 % Allowed : 14.02 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.67 (0.17), residues: 2552 helix: 1.81 (0.13), residues: 1564 sheet: 0.87 (0.50), residues: 112 loop : -2.28 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 692 HIS 0.016 0.002 HIS A 256 PHE 0.012 0.001 PHE D 590 TYR 0.016 0.002 TYR B 451 ARG 0.004 0.000 ARG C 462 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8016 (tpp80) cc_final: 0.7564 (mtm-85) REVERT: A 581 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8504 (mptm) REVERT: A 716 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8013 (ttm-80) REVERT: B 188 ARG cc_start: 0.7974 (tpp80) cc_final: 0.7505 (mtm-85) REVERT: B 256 HIS cc_start: 0.6633 (OUTLIER) cc_final: 0.5758 (m-70) REVERT: B 716 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8005 (ttm-80) REVERT: C 188 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7461 (mtm-85) REVERT: C 256 HIS cc_start: 0.6843 (OUTLIER) cc_final: 0.5722 (m-70) REVERT: C 418 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: C 716 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7437 (ttm-80) REVERT: D 188 ARG cc_start: 0.8015 (tpp80) cc_final: 0.7397 (mtm-85) REVERT: D 696 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7878 (ttt180) outliers start: 19 outliers final: 7 residues processed: 173 average time/residue: 3.1300 time to fit residues: 616.4132 Evaluate side-chains 161 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 696 ARG Chi-restraints excluded: chain D residue 721 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22932 Z= 0.254 Angle : 0.596 11.249 30712 Z= 0.311 Chirality : 0.068 1.663 3308 Planarity : 0.004 0.083 3700 Dihedral : 19.630 178.901 4160 Min Nonbonded Distance : 1.339 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.62 % Favored : 92.91 % Rotamer: Outliers : 0.71 % Allowed : 14.37 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.69 (0.17), residues: 2552 helix: 1.84 (0.13), residues: 1556 sheet: 0.92 (0.50), residues: 112 loop : -2.28 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 692 HIS 0.012 0.002 HIS D 471 PHE 0.012 0.001 PHE D 590 TYR 0.016 0.002 TYR B 451 ARG 0.004 0.000 ARG A 696 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8020 (tpp80) cc_final: 0.7570 (mtm-85) REVERT: A 581 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8447 (mptm) REVERT: A 716 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8004 (ttm-80) REVERT: B 188 ARG cc_start: 0.7976 (tpp80) cc_final: 0.7507 (mtm-85) REVERT: B 256 HIS cc_start: 0.6817 (OUTLIER) cc_final: 0.5727 (m-70) REVERT: B 716 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7916 (ttm-80) REVERT: C 188 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7460 (mtm-85) REVERT: C 256 HIS cc_start: 0.6868 (OUTLIER) cc_final: 0.5781 (m-70) REVERT: C 418 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: C 716 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7441 (ttm-80) REVERT: D 188 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7400 (mtm-85) REVERT: D 696 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7877 (ttt180) outliers start: 16 outliers final: 7 residues processed: 165 average time/residue: 3.0566 time to fit residues: 573.7517 Evaluate side-chains 162 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 696 ARG Chi-restraints excluded: chain D residue 721 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 394 ASN A 471 HIS C 279 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.104985 restraints weight = 82472.317| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.77 r_work: 0.3148 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22932 Z= 0.163 Angle : 0.533 11.046 30712 Z= 0.280 Chirality : 0.064 1.566 3308 Planarity : 0.003 0.048 3700 Dihedral : 18.434 177.753 4160 Min Nonbonded Distance : 1.423 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.96 % Favored : 93.61 % Rotamer: Outliers : 0.84 % Allowed : 14.02 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.99 (0.17), residues: 2552 helix: 2.12 (0.13), residues: 1560 sheet: 0.87 (0.49), residues: 112 loop : -2.24 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 739 HIS 0.010 0.001 HIS D 256 PHE 0.009 0.001 PHE B 449 TYR 0.014 0.001 TYR B 451 ARG 0.003 0.000 ARG C 462 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13171.70 seconds wall clock time: 233 minutes 0.71 seconds (13980.71 seconds total)