Starting phenix.real_space_refine on Fri Aug 7 16:25:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pj6_71681/08_2026/9pj6_71681.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pj6_71681/08_2026/9pj6_71681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pj6_71681/08_2026/9pj6_71681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pj6_71681/08_2026/9pj6_71681.map" model { file = "/net/cci-nas-00/data/ceres_data/9pj6_71681/08_2026/9pj6_71681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pj6_71681/08_2026/9pj6_71681.cif" } resolution = 2.97 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= 0.001 sd= 0.029 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: 6 Type Number sf(0) Gaussians P 32 5.49 5 S 128 5.16 5 Na 4 4.78 5 C 14628 2.51 5 N 3400 2.21 5 O 3920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22112 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5098 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 16, 'TRANS': 610} Chain breaks: 2 Chain: "B" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5098 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 16, 'TRANS': 610} Chain breaks: 2 Chain: "C" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5098 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 16, 'TRANS': 610} Chain breaks: 2 Chain: "D" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5098 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 16, 'TRANS': 610} Chain breaks: 2 Chain: "A" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 522 Unusual residues: {' NA': 2, 'POV': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 314 Unusual residues: {' NA': 2, 'POV': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 4.83, per 1000 atoms: 0.22 Number of scatterers: 22112 At special positions: 0 Unit cell: (151.11, 151.11, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 128 16.00 P 32 15.00 Na 4 11.00 O 3920 8.00 N 3400 7.00 C 14628 6.00 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: 1.65 Conformation dependent library (CDL) restraints added in 855.6 milliseconds 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4792 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 64.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 131 through 145 removed outlier: 3.617A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 149 removed outlier: 3.781A pdb=" N ARG A 149 " --> pdb=" O CYS A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.606A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.511A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.504A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.536A pdb=" N ALA A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.535A pdb=" N LEU A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.693A pdb=" N THR A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.530A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.528A 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 409 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.510A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 4.014A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.558A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 504 removed outlier: 3.730A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.853A pdb=" N ILE A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 542 removed outlier: 3.822A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.894A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.850A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 606 removed outlier: 3.655A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 637 removed outlier: 3.523A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 650 through 677 removed outlier: 3.640A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 707 removed outlier: 3.759A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'B' and resid 119 through 130 Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.617A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 removed outlier: 3.781A pdb=" N ARG B 149 " --> pdb=" O CYS B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.606A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.512A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.504A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.535A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.534A pdb=" N LEU B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 331 through 336 removed outlier: 3.693A pdb=" N THR B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.530A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.528A 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 409 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.511A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 4.014A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.557A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 504 removed outlier: 3.729A pdb=" N ARG B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.853A pdb=" N ILE B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 542 removed outlier: 3.821A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.894A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.851A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 606 removed outlier: 3.655A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 637 removed outlier: 3.523A pdb=" N LEU B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 647 Processing helix chain 'B' and resid 650 through 677 removed outlier: 3.638A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 707 removed outlier: 3.759A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.501A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.618A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 144 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 149 removed outlier: 3.781A pdb=" N ARG C 149 " --> pdb=" O CYS C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.606A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.511A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.503A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.534A pdb=" N ALA C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.535A pdb=" N LEU C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 331 through 336 removed outlier: 3.693A pdb=" N THR C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.530A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 removed outlier: 3.528A 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 409 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.511A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 4.014A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.557A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 504 removed outlier: 3.730A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 517 removed outlier: 3.853A pdb=" N ILE C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 542 removed outlier: 3.821A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.894A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.851A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 606 removed outlier: 3.655A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 637 removed outlier: 3.523A pdb=" N LEU C 632 " --> pdb=" O ALA C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 647 Processing helix chain 'C' and resid 650 through 677 removed outlier: 3.638A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 707 removed outlier: 3.759A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 131 through 145 removed outlier: 3.617A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 144 " --> pdb=" O VAL D 140 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.781A pdb=" N ARG D 149 " --> pdb=" O CYS D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 153 through 159 removed outlier: 3.605A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.512A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.504A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.535A pdb=" N ALA D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.534A pdb=" N LEU D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 331 through 336 removed outlier: 3.692A pdb=" N THR D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.530A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.528A 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 409 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.511A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 4.014A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.557A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 504 removed outlier: 3.729A pdb=" N ARG D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 517 removed outlier: 3.853A pdb=" N ILE D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 removed outlier: 3.821A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.895A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.851A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 606 removed outlier: 3.655A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 595 " --> pdb=" O LEU D 591 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 637 removed outlier: 3.523A pdb=" N LEU D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 647 Processing helix chain 'D' and resid 650 through 677 removed outlier: 3.638A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 707 removed outlier: 3.759A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.763A pdb=" N LYS A 376 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP A 391 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 6.947A 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: 6.763A pdb=" N LYS B 376 " --> pdb=" O ASP B 391 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP B 391 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 6.947A 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: 6.763A pdb=" N LYS C 376 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP C 391 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 6.946A 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: 6.763A pdb=" N LYS D 376 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP D 391 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2913 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3320 1.31 - 1.43: 5878 1.43 - 1.56: 12995 1.56 - 1.68: 71 1.68 - 1.81: 212 Bond restraints: 22476 Sorted by residual: bond pdb=" C21 POV B 904 " pdb=" O21 POV B 904 " ideal model delta sigma weight residual 1.330 1.424 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C21 POV B 905 " pdb=" O21 POV B 905 " ideal model delta sigma weight residual 1.330 1.424 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C21 POV D 905 " pdb=" O21 POV D 905 " ideal model delta sigma weight residual 1.330 1.424 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C21 POV C 905 " pdb=" O21 POV C 905 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C21 POV A 904 " pdb=" O21 POV A 904 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.00e-02 2.50e+03 2.15e+01 ... (remaining 22471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 28617 2.62 - 5.25: 987 5.25 - 7.87: 288 7.87 - 10.49: 119 10.49 - 13.11: 77 Bond angle restraints: 30088 Sorted by residual: angle pdb=" C LEU B 422 " pdb=" N GLU B 423 " pdb=" CA GLU B 423 " ideal model delta sigma weight residual 120.09 127.14 -7.05 1.25e+00 6.40e-01 3.18e+01 angle pdb=" C LEU D 422 " pdb=" N GLU D 423 " pdb=" CA GLU D 423 " ideal model delta sigma weight residual 120.09 127.12 -7.03 1.25e+00 6.40e-01 3.16e+01 angle pdb=" C LEU C 422 " pdb=" N GLU C 423 " pdb=" CA GLU C 423 " ideal model delta sigma weight residual 120.09 127.10 -7.01 1.25e+00 6.40e-01 3.15e+01 angle pdb=" C LEU A 422 " pdb=" N GLU A 423 " pdb=" CA GLU A 423 " ideal model delta sigma weight residual 120.09 127.06 -6.97 1.25e+00 6.40e-01 3.11e+01 angle pdb=" N GLN A 514 " pdb=" CA GLN A 514 " pdb=" C GLN A 514 " ideal model delta sigma weight residual 110.80 122.63 -11.83 2.13e+00 2.20e-01 3.08e+01 ... (remaining 30083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.97: 12990 31.97 - 63.93: 635 63.93 - 95.90: 109 95.90 - 127.86: 30 127.86 - 159.83: 28 Dihedral angle restraints: 13792 sinusoidal: 6412 harmonic: 7380 Sorted by residual: dihedral pdb=" CA LEU C 513 " pdb=" C LEU C 513 " pdb=" N GLN C 514 " pdb=" CA GLN C 514 " ideal model delta harmonic sigma weight residual -180.00 -142.64 -37.36 0 5.00e+00 4.00e-02 5.58e+01 dihedral pdb=" CA LEU A 513 " pdb=" C LEU A 513 " pdb=" N GLN A 514 " pdb=" CA GLN A 514 " ideal model delta harmonic sigma weight residual -180.00 -142.68 -37.32 0 5.00e+00 4.00e-02 5.57e+01 dihedral pdb=" CA LEU D 513 " pdb=" C LEU D 513 " pdb=" N GLN D 514 " pdb=" CA GLN D 514 " ideal model delta harmonic sigma weight residual -180.00 -142.73 -37.27 0 5.00e+00 4.00e-02 5.56e+01 ... (remaining 13789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2333 0.051 - 0.102: 775 0.102 - 0.152: 104 0.152 - 0.203: 32 0.203 - 0.254: 8 Chirality restraints: 3252 Sorted by residual: chirality pdb=" CG LEU C 517 " pdb=" CB LEU C 517 " pdb=" CD1 LEU C 517 " pdb=" CD2 LEU C 517 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU B 517 " pdb=" CB LEU B 517 " pdb=" CD1 LEU B 517 " pdb=" CD2 LEU B 517 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CG LEU A 517 " pdb=" CB LEU A 517 " pdb=" CD1 LEU A 517 " pdb=" CD2 LEU A 517 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 3249 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 509 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.73e+00 pdb=" N PRO D 510 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 510 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 510 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 509 " 0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO A 510 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 509 " 0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO B 510 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 510 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 510 " 0.033 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1615 2.74 - 3.28: 19797 3.28 - 3.82: 34829 3.82 - 4.36: 44754 4.36 - 4.90: 76123 Nonbonded interactions: 177118 Sorted by model distance: nonbonded pdb="NA NA A 911 " pdb="NA NA A 912 " model vdw 2.198 1.900 nonbonded pdb=" O PRO C 753 " pdb=" OH TYR D 213 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" O PRO D 753 " model vdw 2.277 3.040 nonbonded pdb=" O PRO A 753 " pdb=" OH TYR B 213 " model vdw 2.302 3.040 nonbonded pdb=" O PRO B 753 " pdb=" OH TYR C 213 " model vdw 2.307 3.040 ... (remaining 177113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 118 through 906) selection = (chain 'B' and resid 118 through 906) selection = (chain 'C' and resid 118 through 906) selection = (chain 'D' and resid 118 through 906) } 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: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 19.440 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:9.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 : 0.011 0.094 22480 Z= 0.505 Angle : 1.422 13.114 30096 Z= 0.613 Chirality : 0.051 0.254 3252 Planarity : 0.006 0.060 3600 Dihedral : 20.345 159.825 8988 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.12 % Favored : 93.56 % Rotamer: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.58 % 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 are not related in a simple way. whole: -5.77 (0.11), residues: 2484 helix: -4.20 (0.06), residues: 1556 sheet: -1.29 (0.45), residues: 112 loop : -2.89 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 698 TYR 0.020 0.003 TYR D 451 PHE 0.041 0.003 PHE A 633 TRP 0.028 0.002 TRP B 692 HIS 0.013 0.003 HIS C 471 Details of bonding type rmsd/Z covalent geometry : bond 0.01064 / 0.51 (22476) covalent geometry : angle 1.42208 / 0.61 (30088) SS BOND : bond 0.00728 / 0.36 ( 4) SS BOND : angle 0.75644 / 0.45 ( 8) hydrogen bonds : bond 0.31223 / 20.49 ( 995) hydrogen bonds : angle 9.15030 / 6.30 ( 2913) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 528 time to evaluate : 0.650 Fit side-chains REVERT: A 121 LYS cc_start: 0.7934 (mptt) cc_final: 0.7146 (ttpp) REVERT: A 285 GLU cc_start: 0.7071 (mp0) cc_final: 0.6856 (mp0) REVERT: A 332 GLU cc_start: 0.7456 (tt0) cc_final: 0.7150 (tp30) REVERT: A 495 MET cc_start: 0.6982 (mtm) cc_final: 0.6598 (mmt) REVERT: A 529 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8052 (tm-30) REVERT: A 581 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7214 (tmtt) REVERT: A 716 ARG cc_start: 0.7359 (ttp-170) cc_final: 0.6610 (mmt180) REVERT: A 743 LYS cc_start: 0.8445 (ptpt) cc_final: 0.8233 (ptmt) REVERT: B 121 LYS cc_start: 0.8092 (mptt) cc_final: 0.7365 (ttpp) REVERT: B 332 GLU cc_start: 0.7412 (tt0) cc_final: 0.7159 (tp30) REVERT: B 495 MET cc_start: 0.6978 (mtm) cc_final: 0.6766 (mmt) REVERT: B 581 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7441 (tmtt) REVERT: B 716 ARG cc_start: 0.7381 (ttp-170) cc_final: 0.6724 (mmt180) REVERT: C 121 LYS cc_start: 0.7911 (mptt) cc_final: 0.7120 (ttpp) REVERT: C 285 GLU cc_start: 0.7079 (mp0) cc_final: 0.6836 (mp0) REVERT: C 332 GLU cc_start: 0.7517 (tt0) cc_final: 0.7126 (tp30) REVERT: C 346 GLN cc_start: 0.8980 (mt0) cc_final: 0.8772 (mt0) REVERT: C 495 MET cc_start: 0.6927 (mtm) cc_final: 0.6534 (mmt) REVERT: C 529 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8083 (tm-30) REVERT: C 581 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7119 (tmtt) REVERT: C 716 ARG cc_start: 0.7352 (ttp-170) cc_final: 0.6567 (mmt180) REVERT: C 743 LYS cc_start: 0.8427 (ptpt) cc_final: 0.8194 (ptmt) REVERT: D 121 LYS cc_start: 0.7944 (mptt) cc_final: 0.7093 (ttpp) REVERT: D 285 GLU cc_start: 0.7162 (mp0) cc_final: 0.6959 (mp0) REVERT: D 332 GLU cc_start: 0.7481 (tt0) cc_final: 0.7173 (tp30) REVERT: D 495 MET cc_start: 0.6963 (mtm) cc_final: 0.6658 (mmt) REVERT: D 529 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8162 (tm-30) REVERT: D 581 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7257 (tmtt) REVERT: D 716 ARG cc_start: 0.7375 (ttp-170) cc_final: 0.6679 (mmt180) outliers start: 4 outliers final: 0 residues processed: 532 average time/residue: 0.6815 time to fit residues: 405.8349 Evaluate side-chains 358 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.0040 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 274 GLN A 279 GLN A 314 ASN A 671 ASN A 735 ASN B 227 GLN B 274 GLN B 279 GLN B 314 ASN B 671 ASN B 735 ASN C 227 GLN C 274 GLN C 279 GLN C 314 ASN C 671 ASN C 735 ASN D 227 GLN D 274 GLN D 279 GLN D 314 ASN D 671 ASN D 735 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.178761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.133166 restraints weight = 22970.003| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.84 r_work: 0.3029 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22480 Z= 0.125 Angle : 0.648 10.640 30096 Z= 0.322 Chirality : 0.039 0.175 3252 Planarity : 0.005 0.039 3600 Dihedral : 24.181 168.544 4092 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.23 % Favored : 94.61 % Rotamer: Outliers : 1.85 % Allowed : 10.50 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.15), residues: 2484 helix: -1.43 (0.11), residues: 1572 sheet: -1.33 (0.47), residues: 120 loop : -2.53 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 487 TYR 0.014 0.002 TYR B 540 PHE 0.027 0.001 PHE C 449 TRP 0.017 0.001 TRP B 692 HIS 0.007 0.002 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (22476) covalent geometry : angle 0.64794 / 0.32 (30088) SS BOND : bond 0.00079 / 0.04 ( 4) SS BOND : angle 0.36625 / 0.24 ( 8) hydrogen bonds : bond 0.05016 / 3.22 ( 995) hydrogen bonds : angle 3.92868 / 2.68 ( 2913) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 382 time to evaluate : 0.620 Fit side-chains REVERT: A 285 GLU cc_start: 0.7494 (mp0) cc_final: 0.7292 (mp0) REVERT: A 332 GLU cc_start: 0.8152 (tt0) cc_final: 0.7853 (tp30) REVERT: A 495 MET cc_start: 0.7742 (mtm) cc_final: 0.6998 (mmt) REVERT: A 581 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7566 (tmtt) REVERT: A 586 ASP cc_start: 0.7170 (t0) cc_final: 0.6676 (m-30) REVERT: A 664 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7850 (tt) REVERT: A 716 ARG cc_start: 0.7642 (ttp-170) cc_final: 0.6633 (mmt180) REVERT: B 332 GLU cc_start: 0.8141 (tt0) cc_final: 0.7849 (tp30) REVERT: B 495 MET cc_start: 0.7745 (mtm) cc_final: 0.7004 (mmt) REVERT: B 581 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7560 (tmtt) REVERT: B 586 ASP cc_start: 0.7091 (t0) cc_final: 0.6665 (m-30) REVERT: B 664 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7874 (tt) REVERT: B 716 ARG cc_start: 0.7634 (ttp-170) cc_final: 0.6616 (mmt180) REVERT: C 332 GLU cc_start: 0.8157 (tt0) cc_final: 0.7853 (tp30) REVERT: C 495 MET cc_start: 0.7781 (mtm) cc_final: 0.6981 (mmt) REVERT: C 581 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7557 (tmtt) REVERT: C 586 ASP cc_start: 0.7151 (t0) cc_final: 0.6659 (m-30) REVERT: C 664 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7854 (tt) REVERT: C 716 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.6626 (mmt180) REVERT: D 285 GLU cc_start: 0.7528 (mp0) cc_final: 0.7314 (mp0) REVERT: D 332 GLU cc_start: 0.8156 (tt0) cc_final: 0.7851 (tp30) REVERT: D 495 MET cc_start: 0.7792 (mtm) cc_final: 0.7015 (mmt) REVERT: D 581 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7535 (tmtt) REVERT: D 586 ASP cc_start: 0.7207 (t0) cc_final: 0.6769 (m-30) REVERT: D 644 ILE cc_start: 0.8148 (mt) cc_final: 0.7803 (tt) REVERT: D 716 ARG cc_start: 0.7668 (ttp-170) cc_final: 0.6634 (mmt180) outliers start: 41 outliers final: 7 residues processed: 406 average time/residue: 0.5935 time to fit residues: 274.3942 Evaluate side-chains 324 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 314 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 159 optimal weight: 0.0000 chunk 223 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS B 523 HIS B 585 HIS C 523 HIS C 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.171280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.122726 restraints weight = 23284.493| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.83 r_work: 0.2992 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22480 Z= 0.110 Angle : 0.583 10.190 30096 Z= 0.288 Chirality : 0.038 0.129 3252 Planarity : 0.004 0.038 3600 Dihedral : 22.697 165.926 4092 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.87 % Favored : 94.81 % Rotamer: Outliers : 2.52 % Allowed : 11.22 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.17), residues: 2484 helix: -0.19 (0.13), residues: 1644 sheet: -0.83 (0.49), residues: 112 loop : -2.68 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 487 TYR 0.017 0.002 TYR C 540 PHE 0.025 0.001 PHE B 449 TRP 0.010 0.001 TRP A 692 HIS 0.007 0.002 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (22476) covalent geometry : angle 0.58273 / 0.29 (30088) SS BOND : bond 0.00021 / 0.01 ( 4) SS BOND : angle 0.36985 / 0.23 ( 8) hydrogen bonds : bond 0.03932 / 2.50 ( 995) hydrogen bonds : angle 3.51299 / 2.41 ( 2913) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 330 time to evaluate : 0.817 Fit side-chains REVERT: A 121 LYS cc_start: 0.7725 (mptp) cc_final: 0.7029 (ttpp) REVERT: A 285 GLU cc_start: 0.7537 (mp0) cc_final: 0.7321 (mp0) REVERT: A 332 GLU cc_start: 0.8237 (tt0) cc_final: 0.7841 (tp30) REVERT: A 431 MET cc_start: 0.8179 (mtp) cc_final: 0.7317 (mmt) REVERT: A 495 MET cc_start: 0.7700 (mtm) cc_final: 0.6936 (mmt) REVERT: A 581 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7436 (tmtt) REVERT: A 716 ARG cc_start: 0.7631 (ttp-170) cc_final: 0.6657 (tpm170) REVERT: A 747 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.8167 (p) REVERT: B 332 GLU cc_start: 0.8222 (tt0) cc_final: 0.7834 (tp30) REVERT: B 431 MET cc_start: 0.8217 (mtp) cc_final: 0.7341 (mmt) REVERT: B 495 MET cc_start: 0.7682 (mtm) cc_final: 0.6911 (mmt) REVERT: B 581 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7423 (tmtt) REVERT: B 716 ARG cc_start: 0.7609 (ttp-170) cc_final: 0.6633 (tpm170) REVERT: B 747 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8161 (p) REVERT: C 332 GLU cc_start: 0.8246 (tt0) cc_final: 0.7851 (tp30) REVERT: C 431 MET cc_start: 0.8201 (mtp) cc_final: 0.7342 (mmt) REVERT: C 495 MET cc_start: 0.7747 (mtm) cc_final: 0.6950 (mmt) REVERT: C 581 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7459 (tmtt) REVERT: C 586 ASP cc_start: 0.7096 (t0) cc_final: 0.6742 (m-30) REVERT: C 716 ARG cc_start: 0.7608 (ttp-170) cc_final: 0.6683 (tpm170) REVERT: C 747 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8141 (p) REVERT: D 122 ARG cc_start: 0.7284 (mtm180) cc_final: 0.7052 (mtm-85) REVERT: D 285 GLU cc_start: 0.7559 (mp0) cc_final: 0.7344 (mp0) REVERT: D 332 GLU cc_start: 0.8245 (tt0) cc_final: 0.7858 (tp30) REVERT: D 431 MET cc_start: 0.8199 (mtp) cc_final: 0.7330 (mmt) REVERT: D 495 MET cc_start: 0.7742 (mtm) cc_final: 0.7000 (mmt) REVERT: D 581 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7375 (tmtt) REVERT: D 586 ASP cc_start: 0.7104 (t0) cc_final: 0.6811 (m-30) REVERT: D 644 ILE cc_start: 0.8059 (mt) cc_final: 0.7706 (tt) REVERT: D 716 ARG cc_start: 0.7612 (ttp-170) cc_final: 0.6669 (tpm170) REVERT: D 747 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8161 (p) outliers start: 56 outliers final: 4 residues processed: 358 average time/residue: 0.6686 time to fit residues: 269.9054 Evaluate side-chains 317 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 309 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 189 optimal weight: 4.9990 chunk 39 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.173015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.126878 restraints weight = 23494.553| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.81 r_work: 0.3016 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 22480 Z= 0.099 Angle : 0.535 10.187 30096 Z= 0.264 Chirality : 0.037 0.126 3252 Planarity : 0.003 0.036 3600 Dihedral : 21.135 165.576 4092 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 2.16 % Allowed : 12.16 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2484 helix: 0.47 (0.13), residues: 1632 sheet: -0.55 (0.49), residues: 112 loop : -2.56 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 202 TYR 0.017 0.001 TYR A 540 PHE 0.021 0.001 PHE C 449 TRP 0.009 0.001 TRP A 692 HIS 0.006 0.001 HIS C 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (22476) covalent geometry : angle 0.53488 / 0.26 (30088) SS BOND : bond 0.00038 / 0.02 ( 4) SS BOND : angle 0.35592 / 0.23 ( 8) hydrogen bonds : bond 0.03363 / 2.14 ( 995) hydrogen bonds : angle 3.36849 / 2.32 ( 2913) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 330 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7692 (mptp) cc_final: 0.6973 (ttpp) REVERT: A 122 ARG cc_start: 0.7378 (mtm180) cc_final: 0.7143 (mtm-85) REVERT: A 257 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7554 (mp0) REVERT: A 285 GLU cc_start: 0.7546 (mp0) cc_final: 0.7297 (mp0) REVERT: A 495 MET cc_start: 0.7817 (mtm) cc_final: 0.7102 (mmt) REVERT: A 574 MET cc_start: 0.8207 (mtp) cc_final: 0.7902 (mpp) REVERT: A 581 LYS cc_start: 0.8259 (ttmt) cc_final: 0.7612 (tmtt) REVERT: A 716 ARG cc_start: 0.7671 (ttp-170) cc_final: 0.6724 (tpm170) REVERT: A 717 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.6808 (mtm) REVERT: A 747 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.8222 (p) REVERT: B 121 LYS cc_start: 0.7640 (mptp) cc_final: 0.6902 (ttpp) REVERT: B 122 ARG cc_start: 0.7357 (mtm180) cc_final: 0.7087 (mtm-85) REVERT: B 257 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7598 (mp0) REVERT: B 495 MET cc_start: 0.7820 (mtm) cc_final: 0.7109 (mmt) REVERT: B 574 MET cc_start: 0.8210 (mtp) cc_final: 0.7864 (mpp) REVERT: B 578 MET cc_start: 0.8430 (mtm) cc_final: 0.8085 (mtp) REVERT: B 581 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7589 (tmtt) REVERT: B 716 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.6710 (tpm170) REVERT: B 717 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.6817 (mtm) REVERT: B 747 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.8217 (p) REVERT: C 121 LYS cc_start: 0.7676 (mptp) cc_final: 0.6981 (ttpp) REVERT: C 257 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7582 (mp0) REVERT: C 495 MET cc_start: 0.7861 (mtm) cc_final: 0.7131 (mmt) REVERT: C 574 MET cc_start: 0.8242 (mtp) cc_final: 0.7893 (mpp) REVERT: C 578 MET cc_start: 0.8388 (mtt) cc_final: 0.8038 (mtp) REVERT: C 581 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7584 (tmtt) REVERT: C 716 ARG cc_start: 0.7642 (ttp-170) cc_final: 0.6743 (tpm170) REVERT: C 747 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8210 (p) REVERT: D 122 ARG cc_start: 0.7334 (mtm180) cc_final: 0.7065 (mtm-85) REVERT: D 495 MET cc_start: 0.7859 (mtm) cc_final: 0.7192 (mmt) REVERT: D 578 MET cc_start: 0.8414 (mtt) cc_final: 0.8068 (mtp) REVERT: D 581 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7577 (tmtt) REVERT: D 644 ILE cc_start: 0.8103 (mt) cc_final: 0.7767 (tt) REVERT: D 716 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.6734 (tpm170) REVERT: D 747 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8226 (p) outliers start: 48 outliers final: 16 residues processed: 351 average time/residue: 0.6914 time to fit residues: 273.6878 Evaluate side-chains 330 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 308 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 233 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.166352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.119040 restraints weight = 23406.924| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.85 r_work: 0.2940 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22480 Z= 0.160 Angle : 0.619 10.123 30096 Z= 0.303 Chirality : 0.040 0.136 3252 Planarity : 0.004 0.038 3600 Dihedral : 20.715 168.339 4092 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.15 % Favored : 94.52 % Rotamer: Outliers : 3.06 % Allowed : 12.03 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2484 helix: 0.56 (0.13), residues: 1624 sheet: -0.34 (0.49), residues: 112 loop : -2.39 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 487 TYR 0.020 0.002 TYR C 451 PHE 0.021 0.002 PHE C 449 TRP 0.008 0.001 TRP A 692 HIS 0.007 0.002 HIS D 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (22476) covalent geometry : angle 0.61882 / 0.30 (30088) SS BOND : bond 0.00067 / 0.03 ( 4) SS BOND : angle 0.55063 / 0.35 ( 8) hydrogen bonds : bond 0.04134 / 2.64 ( 995) hydrogen bonds : angle 3.47760 / 2.39 ( 2913) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 317 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7674 (mptp) cc_final: 0.6970 (ttpp) REVERT: A 122 ARG cc_start: 0.7394 (mtm180) cc_final: 0.7119 (mtm-85) REVERT: A 188 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7564 (mtt-85) REVERT: A 431 MET cc_start: 0.8265 (mtp) cc_final: 0.7404 (mmt) REVERT: A 495 MET cc_start: 0.7848 (mtm) cc_final: 0.7160 (mmt) REVERT: A 581 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7639 (tmtt) REVERT: A 716 ARG cc_start: 0.7647 (ttp-170) cc_final: 0.6718 (tpm170) REVERT: A 747 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8245 (p) REVERT: B 121 LYS cc_start: 0.7619 (mptp) cc_final: 0.6891 (ttpp) REVERT: B 122 ARG cc_start: 0.7404 (mtm180) cc_final: 0.7097 (mtm-85) REVERT: B 495 MET cc_start: 0.7827 (mtm) cc_final: 0.7148 (mmt) REVERT: B 581 LYS cc_start: 0.8323 (ttmt) cc_final: 0.7622 (tmtt) REVERT: B 716 ARG cc_start: 0.7661 (ttp-170) cc_final: 0.6693 (tpm170) REVERT: B 717 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.6655 (mtt) REVERT: B 747 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8236 (p) REVERT: C 188 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7588 (mtt-85) REVERT: C 431 MET cc_start: 0.8271 (mtp) cc_final: 0.7420 (mmt) REVERT: C 495 MET cc_start: 0.7901 (mtm) cc_final: 0.7165 (mmt) REVERT: C 581 LYS cc_start: 0.8318 (ttmt) cc_final: 0.7616 (tmtt) REVERT: C 716 ARG cc_start: 0.7675 (ttp-170) cc_final: 0.6733 (tpm170) REVERT: C 747 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8235 (p) REVERT: D 122 ARG cc_start: 0.7353 (mtm180) cc_final: 0.7039 (mtm-85) REVERT: D 431 MET cc_start: 0.8274 (mtp) cc_final: 0.7421 (mmt) REVERT: D 495 MET cc_start: 0.7899 (mtm) cc_final: 0.7181 (mmt) REVERT: D 581 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7630 (tmtt) REVERT: D 716 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.6751 (tpm170) REVERT: D 747 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8248 (p) outliers start: 68 outliers final: 25 residues processed: 343 average time/residue: 0.6777 time to fit residues: 262.1968 Evaluate side-chains 332 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 206 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.173072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.125691 restraints weight = 23248.021| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.93 r_work: 0.2966 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22480 Z= 0.105 Angle : 0.537 10.117 30096 Z= 0.266 Chirality : 0.037 0.141 3252 Planarity : 0.003 0.037 3600 Dihedral : 19.979 168.846 4092 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.27 % Favored : 94.57 % Rotamer: Outliers : 2.03 % Allowed : 14.14 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2484 helix: 0.90 (0.13), residues: 1624 sheet: -0.26 (0.48), residues: 112 loop : -2.30 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 487 TYR 0.021 0.002 TYR B 540 PHE 0.019 0.001 PHE B 449 TRP 0.010 0.001 TRP A 692 HIS 0.008 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (22476) covalent geometry : angle 0.53701 / 0.27 (30088) SS BOND : bond 0.00079 / 0.04 ( 4) SS BOND : angle 0.35615 / 0.23 ( 8) hydrogen bonds : bond 0.03269 / 2.08 ( 995) hydrogen bonds : angle 3.34224 / 2.31 ( 2913) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 305 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7561 (mptp) cc_final: 0.6828 (ttpp) REVERT: A 122 ARG cc_start: 0.7383 (mtm180) cc_final: 0.7135 (ttp-110) REVERT: A 431 MET cc_start: 0.8184 (mtp) cc_final: 0.7321 (mmt) REVERT: A 495 MET cc_start: 0.7748 (mtm) cc_final: 0.7042 (mmt) REVERT: A 574 MET cc_start: 0.8241 (mtp) cc_final: 0.7870 (mpp) REVERT: A 578 MET cc_start: 0.8382 (mtm) cc_final: 0.8003 (mtp) REVERT: A 581 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7513 (tmtt) REVERT: A 709 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7258 (pt0) REVERT: A 716 ARG cc_start: 0.7608 (ttp-170) cc_final: 0.6661 (tpm170) REVERT: A 747 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8288 (p) REVERT: B 257 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7646 (mp0) REVERT: B 431 MET cc_start: 0.8172 (mtp) cc_final: 0.7271 (mmt) REVERT: B 495 MET cc_start: 0.7743 (mtm) cc_final: 0.7040 (mmt) REVERT: B 574 MET cc_start: 0.8238 (mtp) cc_final: 0.7877 (mpp) REVERT: B 578 MET cc_start: 0.8355 (mtm) cc_final: 0.7975 (mtp) REVERT: B 581 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7483 (tmtt) REVERT: B 709 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7273 (pt0) REVERT: B 747 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8285 (p) REVERT: C 431 MET cc_start: 0.8228 (mtp) cc_final: 0.7339 (mmt) REVERT: C 495 MET cc_start: 0.7772 (mtm) cc_final: 0.7014 (mmt) REVERT: C 574 MET cc_start: 0.8235 (mtp) cc_final: 0.7858 (mpp) REVERT: C 578 MET cc_start: 0.8370 (mtm) cc_final: 0.7989 (mtp) REVERT: C 581 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7481 (tmtt) REVERT: C 709 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7213 (pt0) REVERT: C 716 ARG cc_start: 0.7595 (ttp-170) cc_final: 0.6643 (tpm170) REVERT: C 747 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8274 (p) REVERT: D 122 ARG cc_start: 0.7408 (mtm180) cc_final: 0.7036 (mtm-85) REVERT: D 431 MET cc_start: 0.8211 (mtp) cc_final: 0.7349 (mmt) REVERT: D 495 MET cc_start: 0.7744 (mtm) cc_final: 0.7052 (mmt) REVERT: D 578 MET cc_start: 0.8359 (mtm) cc_final: 0.7996 (mtp) REVERT: D 581 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7505 (tmtt) REVERT: D 644 ILE cc_start: 0.8056 (mt) cc_final: 0.7709 (tt) REVERT: D 747 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8291 (p) outliers start: 45 outliers final: 21 residues processed: 326 average time/residue: 0.6007 time to fit residues: 221.3991 Evaluate side-chains 317 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 292 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 73 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 75 optimal weight: 0.0570 chunk 77 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN B 330 ASN C 330 ASN D 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.169096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.121683 restraints weight = 23547.763| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.93 r_work: 0.2977 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22480 Z= 0.107 Angle : 0.549 10.059 30096 Z= 0.273 Chirality : 0.038 0.164 3252 Planarity : 0.003 0.039 3600 Dihedral : 19.521 168.834 4092 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.39 % Favored : 94.44 % Rotamer: Outliers : 1.44 % Allowed : 15.14 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2484 helix: 1.10 (0.13), residues: 1608 sheet: -0.21 (0.48), residues: 112 loop : -2.29 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 487 TYR 0.024 0.002 TYR D 540 PHE 0.020 0.001 PHE A 449 TRP 0.009 0.001 TRP D 380 HIS 0.011 0.002 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (22476) covalent geometry : angle 0.54875 / 0.27 (30088) SS BOND : bond 0.00049 / 0.02 ( 4) SS BOND : angle 0.38079 / 0.24 ( 8) hydrogen bonds : bond 0.03254 / 2.07 ( 995) hydrogen bonds : angle 3.34250 / 2.31 ( 2913) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7584 (mptp) cc_final: 0.6862 (ttpp) REVERT: A 122 ARG cc_start: 0.7424 (mtm180) cc_final: 0.7081 (mtm-85) REVERT: A 495 MET cc_start: 0.7795 (mtm) cc_final: 0.7049 (mmt) REVERT: A 574 MET cc_start: 0.8222 (mtp) cc_final: 0.7904 (mpp) REVERT: A 578 MET cc_start: 0.8478 (mtm) cc_final: 0.8093 (mtp) REVERT: A 581 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7586 (tmtt) REVERT: A 709 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7300 (pt0) REVERT: A 747 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8293 (p) REVERT: B 121 LYS cc_start: 0.7636 (mptp) cc_final: 0.6966 (ttpp) REVERT: B 431 MET cc_start: 0.8136 (mtp) cc_final: 0.7347 (mmt) REVERT: B 495 MET cc_start: 0.7793 (mtm) cc_final: 0.7052 (mmt) REVERT: B 574 MET cc_start: 0.8217 (mtp) cc_final: 0.7902 (mpp) REVERT: B 578 MET cc_start: 0.8447 (mtm) cc_final: 0.8053 (mtp) REVERT: B 581 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7576 (tmtt) REVERT: B 709 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7310 (pt0) REVERT: B 747 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8291 (p) REVERT: C 495 MET cc_start: 0.7818 (mtm) cc_final: 0.7086 (mmt) REVERT: C 574 MET cc_start: 0.8253 (mtp) cc_final: 0.7914 (mpp) REVERT: C 578 MET cc_start: 0.8455 (mtm) cc_final: 0.8073 (mtp) REVERT: C 581 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7573 (tmtt) REVERT: C 709 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7241 (pt0) REVERT: C 747 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8291 (p) REVERT: D 122 ARG cc_start: 0.7444 (mtm180) cc_final: 0.7044 (mtm-85) REVERT: D 257 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: D 431 MET cc_start: 0.8221 (mtp) cc_final: 0.7406 (mmt) REVERT: D 495 MET cc_start: 0.7805 (mtm) cc_final: 0.7134 (mmt) REVERT: D 578 MET cc_start: 0.8424 (mtm) cc_final: 0.8065 (mtp) REVERT: D 581 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7574 (tmtt) REVERT: D 644 ILE cc_start: 0.8113 (mt) cc_final: 0.7765 (tt) REVERT: D 709 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7332 (pt0) REVERT: D 747 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8295 (p) outliers start: 32 outliers final: 20 residues processed: 316 average time/residue: 0.5880 time to fit residues: 209.4324 Evaluate side-chains 309 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 284 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 37 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 chunk 209 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 chunk 235 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.170438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.125769 restraints weight = 23343.102| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.74 r_work: 0.3005 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22480 Z= 0.145 Angle : 0.603 10.080 30096 Z= 0.298 Chirality : 0.040 0.164 3252 Planarity : 0.004 0.039 3600 Dihedral : 19.475 169.531 4092 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.31 % Favored : 94.52 % Rotamer: Outliers : 1.98 % Allowed : 15.18 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2484 helix: 0.92 (0.13), residues: 1632 sheet: -0.13 (0.49), residues: 112 loop : -2.23 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 487 TYR 0.027 0.002 TYR C 540 PHE 0.025 0.001 PHE A 592 TRP 0.009 0.001 TRP C 380 HIS 0.013 0.002 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (22476) covalent geometry : angle 0.60331 / 0.30 (30088) SS BOND : bond 0.00070 / 0.03 ( 4) SS BOND : angle 0.48111 / 0.30 ( 8) hydrogen bonds : bond 0.03671 / 2.34 ( 995) hydrogen bonds : angle 3.40277 / 2.35 ( 2913) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 296 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7613 (mptp) cc_final: 0.6937 (ttpp) REVERT: A 122 ARG cc_start: 0.7485 (mtm180) cc_final: 0.7121 (mtm-85) REVERT: A 431 MET cc_start: 0.8283 (mtp) cc_final: 0.7483 (mmt) REVERT: A 487 ARG cc_start: 0.7782 (mtt90) cc_final: 0.7559 (mtt90) REVERT: A 495 MET cc_start: 0.7863 (mtm) cc_final: 0.7132 (mmt) REVERT: A 581 LYS cc_start: 0.8359 (ttmt) cc_final: 0.7697 (tmtt) REVERT: A 747 SER cc_start: 0.8498 (OUTLIER) cc_final: 0.8282 (p) REVERT: B 121 LYS cc_start: 0.7611 (mptp) cc_final: 0.6932 (ttpp) REVERT: B 431 MET cc_start: 0.8236 (mtp) cc_final: 0.7447 (mmt) REVERT: B 495 MET cc_start: 0.7844 (mtm) cc_final: 0.7115 (mmt) REVERT: B 581 LYS cc_start: 0.8362 (ttmt) cc_final: 0.7686 (tmtt) REVERT: B 709 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7360 (pt0) REVERT: B 747 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8288 (p) REVERT: C 431 MET cc_start: 0.8269 (mtp) cc_final: 0.7476 (mmt) REVERT: C 495 MET cc_start: 0.7915 (mtm) cc_final: 0.7207 (mmt) REVERT: C 581 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7689 (tmtt) REVERT: C 709 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7289 (pt0) REVERT: C 747 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8275 (p) REVERT: D 122 ARG cc_start: 0.7501 (mtm180) cc_final: 0.7268 (ttp80) REVERT: D 257 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: D 495 MET cc_start: 0.7858 (mtm) cc_final: 0.7207 (mmt) REVERT: D 581 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7688 (tmtt) REVERT: D 689 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: D 709 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7389 (pt0) REVERT: D 747 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8287 (p) outliers start: 44 outliers final: 23 residues processed: 318 average time/residue: 0.6095 time to fit residues: 219.5288 Evaluate side-chains 320 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 291 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 LYS Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 193 optimal weight: 3.9990 chunk 2 optimal weight: 0.0070 chunk 5 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 222 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.170877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.126184 restraints weight = 23466.521| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.73 r_work: 0.3032 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22480 Z= 0.110 Angle : 0.566 10.045 30096 Z= 0.282 Chirality : 0.038 0.174 3252 Planarity : 0.003 0.039 3600 Dihedral : 19.066 170.305 4092 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 1.53 % Allowed : 16.13 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2484 helix: 1.12 (0.13), residues: 1624 sheet: -0.15 (0.48), residues: 112 loop : -2.19 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 487 TYR 0.027 0.002 TYR D 540 PHE 0.024 0.001 PHE B 449 TRP 0.010 0.001 TRP C 493 HIS 0.015 0.002 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (22476) covalent geometry : angle 0.56601 / 0.28 (30088) SS BOND : bond 0.00062 / 0.03 ( 4) SS BOND : angle 0.34237 / 0.22 ( 8) hydrogen bonds : bond 0.03204 / 2.04 ( 995) hydrogen bonds : angle 3.35100 / 2.32 ( 2913) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 293 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7489 (mtm180) cc_final: 0.7097 (mtm-85) REVERT: A 431 MET cc_start: 0.8257 (mtp) cc_final: 0.7464 (mmt) REVERT: A 495 MET cc_start: 0.7838 (mtm) cc_final: 0.7113 (mmt) REVERT: A 574 MET cc_start: 0.8296 (mtp) cc_final: 0.7998 (mpp) REVERT: A 578 MET cc_start: 0.8475 (mtm) cc_final: 0.8124 (mtp) REVERT: A 581 LYS cc_start: 0.8340 (ttmt) cc_final: 0.7682 (tmtt) REVERT: A 709 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7313 (pt0) REVERT: B 121 LYS cc_start: 0.7608 (mptp) cc_final: 0.6960 (ttpp) REVERT: B 257 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7686 (pm20) REVERT: B 431 MET cc_start: 0.8225 (mtp) cc_final: 0.7436 (mmt) REVERT: B 495 MET cc_start: 0.7813 (mtm) cc_final: 0.7085 (mmt) REVERT: B 574 MET cc_start: 0.8275 (mtp) cc_final: 0.7982 (mpp) REVERT: B 578 MET cc_start: 0.8483 (mtm) cc_final: 0.8111 (mtp) REVERT: B 581 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7645 (tmtt) REVERT: B 664 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8100 (tt) REVERT: B 709 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7372 (pt0) REVERT: C 158 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7474 (tt) REVERT: C 431 MET cc_start: 0.8267 (mtp) cc_final: 0.7476 (mmt) REVERT: C 495 MET cc_start: 0.7893 (mtm) cc_final: 0.7189 (mmt) REVERT: C 578 MET cc_start: 0.8481 (mtm) cc_final: 0.8143 (mtp) REVERT: C 581 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7682 (tmtt) REVERT: C 709 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7282 (pt0) REVERT: D 122 ARG cc_start: 0.7489 (mtm180) cc_final: 0.7256 (ttp80) REVERT: D 257 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8017 (pm20) REVERT: D 431 MET cc_start: 0.8246 (mtp) cc_final: 0.7448 (mmt) REVERT: D 495 MET cc_start: 0.7818 (mtm) cc_final: 0.7148 (mmt) REVERT: D 578 MET cc_start: 0.8445 (mtm) cc_final: 0.8112 (mtp) REVERT: D 581 LYS cc_start: 0.8328 (ttmt) cc_final: 0.7663 (tmtt) REVERT: D 644 ILE cc_start: 0.8165 (mt) cc_final: 0.7812 (tt) REVERT: D 709 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7363 (pt0) outliers start: 34 outliers final: 21 residues processed: 309 average time/residue: 0.5696 time to fit residues: 199.9829 Evaluate side-chains 309 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 284 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 244 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 226 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.0040 chunk 144 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.171843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.127089 restraints weight = 23439.487| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.77 r_work: 0.3036 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22480 Z= 0.104 Angle : 0.549 10.115 30096 Z= 0.275 Chirality : 0.038 0.174 3252 Planarity : 0.003 0.040 3600 Dihedral : 18.595 170.348 4092 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.31 % Allowed : 16.17 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2484 helix: 1.23 (0.13), residues: 1624 sheet: -0.10 (0.49), residues: 112 loop : -2.13 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 122 TYR 0.028 0.001 TYR A 540 PHE 0.023 0.001 PHE A 449 TRP 0.011 0.001 TRP C 493 HIS 0.014 0.002 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (22476) covalent geometry : angle 0.54884 / 0.27 (30088) SS BOND : bond 0.00068 / 0.03 ( 4) SS BOND : angle 0.31114 / 0.21 ( 8) hydrogen bonds : bond 0.03053 / 1.94 ( 995) hydrogen bonds : angle 3.31385 / 2.29 ( 2913) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 305 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7470 (mtm180) cc_final: 0.7065 (mtm-85) REVERT: A 431 MET cc_start: 0.8234 (mtp) cc_final: 0.7436 (mmt) REVERT: A 495 MET cc_start: 0.7781 (mtm) cc_final: 0.7057 (mmt) REVERT: A 578 MET cc_start: 0.8472 (mtm) cc_final: 0.8109 (mtp) REVERT: A 581 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7626 (tmtt) REVERT: A 709 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7300 (pt0) REVERT: B 158 LEU cc_start: 0.7950 (mt) cc_final: 0.7543 (tt) REVERT: B 431 MET cc_start: 0.8178 (mtp) cc_final: 0.7400 (mmt) REVERT: B 495 MET cc_start: 0.7753 (mtm) cc_final: 0.7028 (mmt) REVERT: B 574 MET cc_start: 0.8249 (mtp) cc_final: 0.7956 (mpp) REVERT: B 578 MET cc_start: 0.8461 (mtm) cc_final: 0.8090 (mtp) REVERT: B 581 LYS cc_start: 0.8286 (ttmt) cc_final: 0.7601 (tmtt) REVERT: B 709 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7355 (pt0) REVERT: C 431 MET cc_start: 0.8218 (mtp) cc_final: 0.7414 (mmt) REVERT: C 476 THR cc_start: 0.0917 (OUTLIER) cc_final: 0.0669 (p) REVERT: C 495 MET cc_start: 0.7841 (mtm) cc_final: 0.7131 (mmt) REVERT: C 578 MET cc_start: 0.8445 (mtm) cc_final: 0.8082 (mtp) REVERT: C 581 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7623 (tmtt) REVERT: C 709 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7273 (pt0) REVERT: D 122 ARG cc_start: 0.7492 (mtm180) cc_final: 0.7265 (ttp80) REVERT: D 257 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: D 431 MET cc_start: 0.8240 (mtp) cc_final: 0.7442 (mmt) REVERT: D 495 MET cc_start: 0.7802 (mtm) cc_final: 0.7082 (mmt) REVERT: D 578 MET cc_start: 0.8443 (mtm) cc_final: 0.8091 (mtp) REVERT: D 581 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7582 (tmtt) REVERT: D 644 ILE cc_start: 0.8163 (mt) cc_final: 0.7812 (tt) REVERT: D 709 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7346 (pt0) outliers start: 29 outliers final: 15 residues processed: 321 average time/residue: 0.5328 time to fit residues: 195.0368 Evaluate side-chains 310 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 293 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 686 LYS Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 190 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 210 optimal weight: 0.9990 chunk 148 optimal weight: 0.3980 chunk 218 optimal weight: 4.9990 chunk 247 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.174213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131147 restraints weight = 23226.587| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.66 r_work: 0.3034 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22480 Z= 0.101 Angle : 0.558 10.051 30096 Z= 0.277 Chirality : 0.038 0.175 3252 Planarity : 0.003 0.040 3600 Dihedral : 18.352 170.141 4092 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.68 % Allowed : 17.21 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 2484 helix: 1.38 (0.13), residues: 1608 sheet: -0.04 (0.49), residues: 112 loop : -2.16 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 487 TYR 0.027 0.001 TYR A 540 PHE 0.022 0.001 PHE A 449 TRP 0.013 0.001 TRP C 493 HIS 0.016 0.002 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (22476) covalent geometry : angle 0.55764 / 0.28 (30088) SS BOND : bond 0.00049 / 0.02 ( 4) SS BOND : angle 0.30034 / 0.20 ( 8) hydrogen bonds : bond 0.02970 / 1.89 ( 995) hydrogen bonds : angle 3.27578 / 2.26 ( 2913) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7110.04 seconds wall clock time: 121 minutes 42.95 seconds (7302.95 seconds total)