Starting phenix.real_space_refine on Wed Aug 27 02:23:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6k_42994/08_2025/8v6k_42994_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6k_42994/08_2025/8v6k_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_42994/08_2025/8v6k_42994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6k_42994/08_2025/8v6k_42994.map" model { file = "/net/cci-nas-00/data/ceres_data/8v6k_42994/08_2025/8v6k_42994_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6k_42994/08_2025/8v6k_42994_trim.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 9.13, per 1000 atoms: 0.21 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: 4.24 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.25 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: 10.46 Time building geometry restraints manager: 5.78 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = 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: 1.110 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: 0.340 Extract box with map and model: 0.920 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 42.710 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 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:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.130 ------------------------------------------------------------------------------- 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 22936 Z= 0.303 Angle : 0.998 12.006 30720 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 : 2.16 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.009 0.001 ARG A 716 TYR 0.015 0.002 TYR D 650 PHE 0.015 0.001 PHE D 316 TRP 0.021 0.002 TRP B 739 HIS 0.029 0.002 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00637 (22932) covalent geometry : angle 0.99831 (30712) SS BOND : bond 0.00797 ( 4) SS BOND : angle 0.89465 ( 8) hydrogen bonds : bond 0.27336 ( 1100) hydrogen bonds : angle 8.18515 ( 3228) *********************** 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 : 1.233 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: symmetry clash revert: symmetry clash REVERT: B 562 MET cc_start: 0.7426 (mmm) cc_final: 0.6728 (mmt) outliers start: 4 outliers final: 3 residues processed: 460 average time/residue: 1.6159 time to fit residues: 840.7480 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 : 1.209 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.0570 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- 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 523 HIS D 220 ASN D 227 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.144638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113431 restraints weight = 83877.571| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.75 r_work: 0.3285 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22936 Z= 0.157 Angle : 0.672 11.958 30720 Z= 0.346 Chirality : 0.068 1.673 3308 Planarity : 0.005 0.076 3700 Dihedral : 22.847 178.147 4166 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.62 % Favored : 92.91 % Rotamer: Outliers : 2.03 % Allowed : 9.70 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.16), residues: 2552 helix: 0.55 (0.13), residues: 1568 sheet: 1.35 (0.43), residues: 64 loop : -3.00 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 462 TYR 0.014 0.002 TYR D 575 PHE 0.022 0.002 PHE B 542 TRP 0.017 0.002 TRP B 692 HIS 0.016 0.002 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00356 (22932) covalent geometry : angle 0.66429 (30712) SS BOND : bond 0.00087 ( 4) SS BOND : angle 6.23687 ( 8) hydrogen bonds : bond 0.05157 ( 1100) hydrogen bonds : angle 4.00507 ( 3228) *********************** 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 264 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8950 (mptm) REVERT: B 562 MET cc_start: 0.8693 (mmm) cc_final: 0.8022 (mmt) REVERT: B 682 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8441 (mt-10) REVERT: C 682 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8417 (mt-10) outliers start: 46 outliers final: 6 residues processed: 252 average time/residue: 1.4840 time to fit residues: 429.5497 Evaluate side-chains 177 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 721 CYS Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C 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 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 227 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 chunk 240 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 417 HIS D 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.138082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105378 restraints weight = 83485.015| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.81 r_work: 0.3152 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22936 Z= 0.176 Angle : 0.638 11.234 30720 Z= 0.333 Chirality : 0.068 1.651 3308 Planarity : 0.005 0.081 3700 Dihedral : 21.889 179.512 4160 Min Nonbonded Distance : 1.502 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.47 % Favored : 93.03 % Rotamer: Outliers : 1.81 % Allowed : 10.58 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.17), residues: 2552 helix: 1.25 (0.13), residues: 1604 sheet: 1.46 (0.55), residues: 88 loop : -3.10 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 327 TYR 0.014 0.002 TYR A 451 PHE 0.028 0.002 PHE D 542 TRP 0.014 0.002 TRP A 692 HIS 0.010 0.002 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00401 (22932) covalent geometry : angle 0.63534 (30712) SS BOND : bond 0.00731 ( 4) SS BOND : angle 3.85577 ( 8) hydrogen bonds : bond 0.06022 ( 1100) hydrogen bonds : angle 3.92393 ( 3228) *********************** 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 230 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: A 563 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8113 (mm) REVERT: A 696 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8058 (tmm-80) REVERT: C 562 MET cc_start: 0.8853 (mmt) cc_final: 0.8387 (mmt) REVERT: D 195 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7607 (tp30) REVERT: D 562 MET cc_start: 0.8869 (mmt) cc_final: 0.8508 (mmt) outliers start: 41 outliers final: 7 residues processed: 220 average time/residue: 1.5208 time to fit residues: 383.2531 Evaluate side-chains 169 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 624 SER 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 747 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 B 251 ASN C 394 ASN D 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106465 restraints weight = 83419.878| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.80 r_work: 0.3171 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22936 Z= 0.137 Angle : 0.569 11.256 30720 Z= 0.299 Chirality : 0.066 1.617 3308 Planarity : 0.004 0.075 3700 Dihedral : 20.631 177.052 4160 Min Nonbonded Distance : 1.376 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.19 % Favored : 93.34 % Rotamer: Outliers : 1.41 % Allowed : 11.33 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.17), residues: 2552 helix: 1.71 (0.13), residues: 1600 sheet: 1.62 (0.55), residues: 88 loop : -2.85 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 327 TYR 0.012 0.002 TYR B 451 PHE 0.011 0.001 PHE C 449 TRP 0.011 0.001 TRP D 692 HIS 0.007 0.001 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00309 (22932) covalent geometry : angle 0.56658 (30712) SS BOND : bond 0.00421 ( 4) SS BOND : angle 3.48833 ( 8) hydrogen bonds : bond 0.04761 ( 1100) hydrogen bonds : angle 3.65075 ( 3228) *********************** 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 206 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 HIS cc_start: 0.6187 (OUTLIER) cc_final: 0.5747 (m-70) REVERT: A 479 MET cc_start: 0.3001 (OUTLIER) cc_final: 0.2790 (ttm) REVERT: A 581 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8826 (mptm) REVERT: A 696 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7588 (ttm-80) REVERT: B 418 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: B 479 MET cc_start: 0.3015 (ttt) cc_final: 0.2814 (mtm) REVERT: B 716 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8148 (ttm-80) REVERT: C 256 HIS cc_start: 0.5955 (OUTLIER) cc_final: 0.5700 (m-70) REVERT: C 562 MET cc_start: 0.8837 (mmt) cc_final: 0.8293 (mmt) REVERT: D 256 HIS cc_start: 0.6044 (OUTLIER) cc_final: 0.5551 (m-70) REVERT: D 562 MET cc_start: 0.8876 (mmt) cc_final: 0.8331 (mmt) outliers start: 32 outliers final: 10 residues processed: 199 average time/residue: 1.4008 time to fit residues: 319.7897 Evaluate side-chains 172 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 314 ASN 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 495 MET Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 721 CYS 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 141 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.102544 restraints weight = 83632.946| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.77 r_work: 0.3129 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22936 Z= 0.191 Angle : 0.618 11.239 30720 Z= 0.324 Chirality : 0.069 1.685 3308 Planarity : 0.004 0.104 3700 Dihedral : 20.924 175.701 4160 Min Nonbonded Distance : 1.316 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.97 % Favored : 92.55 % Rotamer: Outliers : 1.81 % Allowed : 11.90 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.17), residues: 2552 helix: 1.64 (0.13), residues: 1576 sheet: 1.01 (0.49), residues: 112 loop : -2.71 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 327 TYR 0.014 0.002 TYR A 451 PHE 0.014 0.002 PHE C 316 TRP 0.012 0.002 TRP A 692 HIS 0.006 0.002 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00444 (22932) covalent geometry : angle 0.61588 (30712) SS BOND : bond 0.00613 ( 4) SS BOND : angle 3.25348 ( 8) hydrogen bonds : bond 0.05737 ( 1100) hydrogen bonds : angle 3.80175 ( 3228) *********************** 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 200 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: A 256 HIS cc_start: 0.6578 (OUTLIER) cc_final: 0.5804 (m-70) REVERT: A 479 MET cc_start: 0.3420 (OUTLIER) cc_final: 0.3207 (ttm) REVERT: A 581 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.8785 (mptm) REVERT: A 716 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8197 (ttm-80) REVERT: B 188 ARG cc_start: 0.8111 (tpp80) cc_final: 0.7588 (mtm-85) REVERT: B 418 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: B 716 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8170 (ttm-80) REVERT: C 256 HIS cc_start: 0.6566 (OUTLIER) cc_final: 0.5843 (m-70) REVERT: D 195 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7580 (tp30) REVERT: D 256 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.5791 (m-70) REVERT: D 418 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: D 479 MET cc_start: 0.3744 (ttt) cc_final: 0.3493 (mtt) REVERT: D 696 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7631 (ttm-80) outliers start: 41 outliers final: 8 residues processed: 191 average time/residue: 1.1767 time to fit residues: 256.7556 Evaluate side-chains 173 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 479 MET 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 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 687 GLU 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 721 CYS Chi-restraints excluded: chain D residue 195 GLU 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 696 ARG Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 200 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 254 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** B 279 GLN D 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104320 restraints weight = 83239.506| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.79 r_work: 0.3142 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22936 Z= 0.150 Angle : 0.567 11.232 30720 Z= 0.298 Chirality : 0.066 1.629 3308 Planarity : 0.004 0.074 3700 Dihedral : 19.947 176.432 4160 Min Nonbonded Distance : 1.388 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.31 % Favored : 93.22 % Rotamer: Outliers : 1.32 % Allowed : 12.70 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.17), residues: 2552 helix: 1.84 (0.13), residues: 1576 sheet: 1.01 (0.49), residues: 112 loop : -2.59 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.014 0.002 TYR B 451 PHE 0.010 0.001 PHE D 590 TRP 0.011 0.001 TRP A 692 HIS 0.007 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00341 (22932) covalent geometry : angle 0.56584 (30712) SS BOND : bond 0.00333 ( 4) SS BOND : angle 2.71039 ( 8) hydrogen bonds : bond 0.04998 ( 1100) hydrogen bonds : angle 3.64676 ( 3228) *********************** 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 193 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8166 (tpp80) cc_final: 0.7657 (mtm-85) REVERT: A 256 HIS cc_start: 0.6798 (OUTLIER) cc_final: 0.5919 (m-70) REVERT: A 581 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8815 (mptm) REVERT: B 188 ARG cc_start: 0.8145 (tpp80) cc_final: 0.7642 (mtm-85) REVERT: B 418 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: B 716 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8175 (ttm-80) REVERT: C 188 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7614 (mtm-85) REVERT: C 256 HIS cc_start: 0.6730 (OUTLIER) cc_final: 0.5935 (m170) REVERT: C 488 MET cc_start: 0.8081 (mtp) cc_final: 0.7719 (mtm) REVERT: C 687 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: C 716 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8197 (ttm-80) REVERT: D 256 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.5830 (m-70) REVERT: D 418 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: D 479 MET cc_start: 0.3753 (ttt) cc_final: 0.3459 (ttm) REVERT: D 488 MET cc_start: 0.8151 (mtp) cc_final: 0.7765 (mtm) REVERT: D 696 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7715 (ttm-80) outliers start: 30 outliers final: 8 residues processed: 188 average time/residue: 1.0647 time to fit residues: 227.5470 Evaluate side-chains 170 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 696 ARG Chi-restraints excluded: chain A residue 721 CYS 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 687 GLU 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 687 GLU Chi-restraints excluded: chain C residue 716 ARG 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 696 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 246 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 279 GLN ** D 471 HIS ** 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 = 0.3783 r_free = 0.3783 target = 0.138985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106476 restraints weight = 83153.163| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.83 r_work: 0.3181 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22936 Z= 0.103 Angle : 0.518 11.049 30720 Z= 0.272 Chirality : 0.063 1.552 3308 Planarity : 0.003 0.055 3700 Dihedral : 18.464 176.783 4160 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.15 % Favored : 93.50 % Rotamer: Outliers : 1.19 % Allowed : 13.14 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.17), residues: 2552 helix: 2.12 (0.13), residues: 1600 sheet: 0.89 (0.49), residues: 112 loop : -2.57 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.012 0.001 TYR B 451 PHE 0.009 0.001 PHE C 449 TRP 0.011 0.001 TRP A 739 HIS 0.008 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00228 (22932) covalent geometry : angle 0.51695 (30712) SS BOND : bond 0.00201 ( 4) SS BOND : angle 1.79552 ( 8) hydrogen bonds : bond 0.04088 ( 1100) hydrogen bonds : angle 3.48045 ( 3228) *********************** 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 203 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8157 (tpp80) cc_final: 0.7656 (mtm-85) REVERT: A 256 HIS cc_start: 0.6732 (OUTLIER) cc_final: 0.5911 (m170) REVERT: A 418 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: A 488 MET cc_start: 0.8105 (mtp) cc_final: 0.7756 (mtm) REVERT: A 581 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.8757 (mptm) REVERT: A 696 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7815 (tmm-80) REVERT: A 716 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8191 (ttm-80) REVERT: B 188 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7669 (mtm-85) REVERT: B 418 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: B 488 MET cc_start: 0.7958 (mtp) cc_final: 0.7603 (mtm) REVERT: B 716 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8181 (ttm-80) REVERT: C 188 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7636 (mtm-85) REVERT: C 256 HIS cc_start: 0.6621 (OUTLIER) cc_final: 0.5868 (m170) REVERT: C 488 MET cc_start: 0.7986 (mtp) cc_final: 0.7650 (mtm) REVERT: C 716 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8247 (ttm-80) REVERT: D 188 ARG cc_start: 0.8103 (tpp80) cc_final: 0.7551 (mtm-85) REVERT: D 256 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.5772 (m170) REVERT: D 418 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: D 479 MET cc_start: 0.3830 (ttt) cc_final: 0.3491 (mtm) REVERT: D 488 MET cc_start: 0.8008 (mtp) cc_final: 0.7639 (mtm) REVERT: D 696 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7672 (ttm-80) outliers start: 27 outliers final: 5 residues processed: 199 average time/residue: 0.9059 time to fit residues: 207.3271 Evaluate side-chains 172 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 HIS 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 418 GLU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 687 GLU 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 256 HIS Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 696 ARG 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 193 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 177 optimal weight: 0.0370 chunk 240 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- 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** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.105842 restraints weight = 83535.038| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.84 r_work: 0.3170 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22936 Z= 0.109 Angle : 0.525 11.177 30720 Z= 0.276 Chirality : 0.064 1.584 3308 Planarity : 0.003 0.053 3700 Dihedral : 18.033 178.123 4160 Min Nonbonded Distance : 1.471 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.61 % Rotamer: Outliers : 0.79 % Allowed : 13.89 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.17), residues: 2552 helix: 2.19 (0.13), residues: 1600 sheet: 0.75 (0.48), residues: 112 loop : -2.50 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 327 TYR 0.013 0.001 TYR B 451 PHE 0.010 0.001 PHE C 449 TRP 0.009 0.001 TRP A 739 HIS 0.012 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00241 (22932) covalent geometry : angle 0.52339 (30712) SS BOND : bond 0.00246 ( 4) SS BOND : angle 2.18676 ( 8) hydrogen bonds : bond 0.04256 ( 1100) hydrogen bonds : angle 3.48519 ( 3228) *********************** 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 169 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7687 (mtm-85) REVERT: A 256 HIS cc_start: 0.6696 (OUTLIER) cc_final: 0.5817 (m170) REVERT: A 418 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: A 488 MET cc_start: 0.8094 (mtp) cc_final: 0.7765 (mtm) REVERT: A 581 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8760 (mptm) REVERT: A 696 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7845 (tmm-80) REVERT: A 716 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8251 (ttm-80) REVERT: B 188 ARG cc_start: 0.8147 (tpp80) cc_final: 0.7654 (mtm-85) REVERT: B 418 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: B 488 MET cc_start: 0.7845 (mtp) cc_final: 0.7542 (mtm) REVERT: B 716 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8173 (ttm-80) REVERT: C 188 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7641 (mtm-85) REVERT: C 488 MET cc_start: 0.7951 (mtp) cc_final: 0.7665 (mtm) REVERT: C 716 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8264 (ttm-80) REVERT: D 188 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7602 (mtm-85) REVERT: D 418 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: D 479 MET cc_start: 0.3847 (ttt) cc_final: 0.3551 (ttm) REVERT: D 488 MET cc_start: 0.7933 (mtp) cc_final: 0.7640 (mtm) REVERT: D 696 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7667 (ttm-80) outliers start: 18 outliers final: 5 residues processed: 167 average time/residue: 0.9877 time to fit residues: 186.5433 Evaluate side-chains 158 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 HIS 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 418 GLU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain C residue 246 LYS 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 696 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 18 optimal weight: 2.9990 chunk 232 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** D 279 GLN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103347 restraints weight = 83059.863| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.83 r_work: 0.3134 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22936 Z= 0.150 Angle : 0.569 11.326 30720 Z= 0.299 Chirality : 0.068 1.665 3308 Planarity : 0.004 0.074 3700 Dihedral : 18.628 177.646 4160 Min Nonbonded Distance : 1.354 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.43 % Favored : 93.10 % Rotamer: Outliers : 0.75 % Allowed : 13.98 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.17), residues: 2552 helix: 2.06 (0.13), residues: 1576 sheet: 0.83 (0.49), residues: 112 loop : -2.47 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 462 TYR 0.014 0.002 TYR A 451 PHE 0.014 0.001 PHE C 316 TRP 0.010 0.001 TRP B 692 HIS 0.011 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00341 (22932) covalent geometry : angle 0.56750 (30712) SS BOND : bond 0.00393 ( 4) SS BOND : angle 2.57679 ( 8) hydrogen bonds : bond 0.05084 ( 1100) hydrogen bonds : angle 3.62860 ( 3228) *********************** 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: 17 poor density : 156 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7718 (mtm-85) REVERT: A 418 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: A 488 MET cc_start: 0.8022 (mtp) cc_final: 0.7803 (mtm) REVERT: A 581 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8831 (mptm) REVERT: A 716 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8179 (ttm-80) REVERT: B 188 ARG cc_start: 0.8172 (tpp80) cc_final: 0.7694 (mtm-85) REVERT: B 418 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: B 488 MET cc_start: 0.7802 (mtp) cc_final: 0.7559 (mtm) REVERT: B 716 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8181 (ttm-80) REVERT: C 188 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7691 (mtm-85) REVERT: C 488 MET cc_start: 0.7912 (mtp) cc_final: 0.7680 (mtm) REVERT: C 716 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8184 (ttm-80) REVERT: D 188 ARG cc_start: 0.8157 (tpp80) cc_final: 0.7631 (mtm-85) REVERT: D 418 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: D 479 MET cc_start: 0.4172 (ttt) cc_final: 0.3850 (ttm) REVERT: D 488 MET cc_start: 0.7898 (mtp) cc_final: 0.7652 (mtm) REVERT: D 696 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7650 (ttm-80) outliers start: 17 outliers final: 7 residues processed: 172 average time/residue: 0.9018 time to fit residues: 176.3732 Evaluate side-chains 163 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 246 LYS Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 716 ARG 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 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 41 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 0.0020 overall best weight: 2.9996 ------------------------------------------------------------------------------- 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** B 279 GLN C 286 GLN D 279 GLN ** 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 = 0.3745 r_free = 0.3745 target = 0.135650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103401 restraints weight = 83460.676| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.79 r_work: 0.3139 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22936 Z= 0.148 Angle : 0.561 11.198 30720 Z= 0.294 Chirality : 0.066 1.621 3308 Planarity : 0.004 0.066 3700 Dihedral : 18.320 177.016 4160 Min Nonbonded Distance : 1.377 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.07 % Favored : 93.46 % Rotamer: Outliers : 0.71 % Allowed : 14.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.17), residues: 2552 helix: 2.04 (0.13), residues: 1580 sheet: 0.87 (0.49), residues: 112 loop : -2.44 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 462 TYR 0.014 0.002 TYR B 451 PHE 0.012 0.001 PHE C 316 TRP 0.009 0.001 TRP A 692 HIS 0.010 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00337 (22932) covalent geometry : angle 0.55957 (30712) SS BOND : bond 0.00342 ( 4) SS BOND : angle 2.52515 ( 8) hydrogen bonds : bond 0.04931 ( 1100) hydrogen bonds : angle 3.60851 ( 3228) ********************** 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 169 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7703 (mtm-85) REVERT: A 256 HIS cc_start: 0.6761 (OUTLIER) cc_final: 0.5738 (m170) REVERT: A 418 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: A 488 MET cc_start: 0.7962 (mtp) cc_final: 0.7760 (mtm) REVERT: A 581 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.8805 (mptm) REVERT: A 716 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8174 (ttm-80) REVERT: B 188 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7666 (mtm-85) REVERT: B 418 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: B 488 MET cc_start: 0.7790 (mtp) cc_final: 0.7569 (mtm) REVERT: B 716 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8177 (ttm-80) REVERT: C 188 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7675 (mtm-85) REVERT: C 488 MET cc_start: 0.7872 (mtp) cc_final: 0.7649 (mtm) REVERT: C 716 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8192 (ttm-80) REVERT: D 188 ARG cc_start: 0.8124 (tpp80) cc_final: 0.7605 (mtm-85) REVERT: D 418 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: D 479 MET cc_start: 0.4088 (ttt) cc_final: 0.3759 (mtm) REVERT: D 488 MET cc_start: 0.7867 (mtp) cc_final: 0.7635 (mtm) REVERT: D 696 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7701 (ttm-80) outliers start: 16 outliers final: 7 residues processed: 168 average time/residue: 0.9154 time to fit residues: 173.7861 Evaluate side-chains 163 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 HIS 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 246 LYS Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 716 ARG 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 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 233 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- 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 B 279 GLN D 279 GLN ** 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 = 0.3758 r_free = 0.3758 target = 0.136752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.104487 restraints weight = 83573.696| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.80 r_work: 0.3159 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22936 Z= 0.120 Angle : 0.532 11.153 30720 Z= 0.280 Chirality : 0.065 1.592 3308 Planarity : 0.003 0.049 3700 Dihedral : 17.642 176.150 4160 Min Nonbonded Distance : 1.423 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.19 % Favored : 93.42 % Rotamer: Outliers : 0.84 % Allowed : 14.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.17), residues: 2552 helix: 2.17 (0.13), residues: 1580 sheet: 0.85 (0.49), residues: 112 loop : -2.41 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 462 TYR 0.013 0.001 TYR A 451 PHE 0.010 0.001 PHE C 449 TRP 0.009 0.001 TRP D 692 HIS 0.010 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00269 (22932) covalent geometry : angle 0.53052 (30712) SS BOND : bond 0.00274 ( 4) SS BOND : angle 2.15703 ( 8) hydrogen bonds : bond 0.04465 ( 1100) hydrogen bonds : angle 3.52921 ( 3228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13467.48 seconds wall clock time: 228 minutes 7.26 seconds (13687.26 seconds total)