Starting phenix.real_space_refine on Mon Sep 23 13:04:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w2h_43748/09_2024/8w2h_43748_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w2h_43748/09_2024/8w2h_43748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w2h_43748/09_2024/8w2h_43748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w2h_43748/09_2024/8w2h_43748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w2h_43748/09_2024/8w2h_43748_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w2h_43748/09_2024/8w2h_43748_trim.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.246 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 44 5.49 5 Mg 4 5.21 5 S 152 5.16 5 C 14752 2.51 5 N 4180 2.21 5 O 4572 1.98 5 H 23240 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 1.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 46944 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 11622 Classifications: {'peptide': 761} Link IDs: {'PTRANS': 20, 'TRANS': 740} Chain: "B" Number of atoms: 11622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 11622 Classifications: {'peptide': 761} Link IDs: {'PTRANS': 20, 'TRANS': 740} Chain: "C" Number of atoms: 11622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 11622 Classifications: {'peptide': 761} Link IDs: {'PTRANS': 20, 'TRANS': 740} Chain: "D" Number of atoms: 11622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 11622 Classifications: {'peptide': 761} Link IDs: {'PTRANS': 20, 'TRANS': 740} Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {' MG': 1, 'ATP': 3, 'FBP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {' MG': 1, 'ATP': 3, 'FBP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {' MG': 1, 'ATP': 3, 'FBP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {' MG': 1, 'ATP': 3, 'FBP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 18.77, per 1000 atoms: 0.40 Number of scatterers: 46944 At special positions: 0 Unit cell: (158.55, 131.25, 129.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 152 16.00 P 44 15.00 Mg 4 11.99 O 4572 8.00 N 4180 7.00 C 14752 6.00 H 23240 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.87 Conformation dependent library (CDL) restraints added in 3.2 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5440 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 25 sheets defined 50.1% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.792A pdb=" N VAL A 73 " --> pdb=" O TRP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 94 through 108 removed outlier: 3.621A pdb=" N ALA A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.597A pdb=" N ILE A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 238 through 254 removed outlier: 3.565A pdb=" N GLY A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 326 Processing helix chain 'A' and resid 348 through 363 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 374 removed outlier: 4.132A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 3.649A pdb=" N HIS A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.608A pdb=" N VAL A 455 " --> pdb=" O TRP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 removed outlier: 3.934A pdb=" N GLY A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 475' Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 497 through 511 Processing helix chain 'A' and resid 512 through 513 No H-bonds generated for 'chain 'A' and resid 512 through 513' Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 600 through 616 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 659 through 663 removed outlier: 3.680A pdb=" N GLN A 662 " --> pdb=" O GLY A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 693 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 722 through 726 Processing helix chain 'A' and resid 739 through 742 removed outlier: 3.648A pdb=" N LEU A 742 " --> pdb=" O GLN A 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 739 through 742' Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.805A pdb=" N MET A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 69 through 74 removed outlier: 3.741A pdb=" N VAL B 73 " --> pdb=" O TRP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 93 Processing helix chain 'B' and resid 94 through 108 removed outlier: 3.624A pdb=" N ALA B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 131 Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.566A pdb=" N ILE B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 238 through 254 removed outlier: 3.567A pdb=" N GLY B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 306 through 326 Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 removed outlier: 4.132A pdb=" N LEU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 removed outlier: 3.649A pdb=" N HIS B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.588A pdb=" N VAL B 455 " --> pdb=" O TRP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 497 through 510 Processing helix chain 'B' and resid 511 through 513 No H-bonds generated for 'chain 'B' and resid 511 through 513' Processing helix chain 'B' and resid 540 through 559 removed outlier: 4.299A pdb=" N ALA B 559 " --> pdb=" O ILE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 588 Processing helix chain 'B' and resid 600 through 617 Processing helix chain 'B' and resid 635 through 647 Processing helix chain 'B' and resid 659 through 663 removed outlier: 3.696A pdb=" N GLN B 662 " --> pdb=" O GLY B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 693 Processing helix chain 'B' and resid 703 through 705 No H-bonds generated for 'chain 'B' and resid 703 through 705' Processing helix chain 'B' and resid 722 through 726 Processing helix chain 'B' and resid 739 through 742 removed outlier: 3.627A pdb=" N LEU B 742 " --> pdb=" O GLN B 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 739 through 742' Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.835A pdb=" N MET B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 54 through 61 Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.727A pdb=" N VAL C 73 " --> pdb=" O TRP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 93 Processing helix chain 'C' and resid 94 through 108 removed outlier: 3.620A pdb=" N ALA C 100 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 108 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 131 Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 177 through 194 removed outlier: 3.604A pdb=" N ILE C 192 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 238 through 254 removed outlier: 3.562A pdb=" N GLY C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 306 through 326 Processing helix chain 'C' and resid 348 through 363 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 369 through 374 removed outlier: 4.130A pdb=" N LEU C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 390 removed outlier: 3.648A pdb=" N HIS C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 428 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 452 through 456 removed outlier: 3.603A pdb=" N VAL C 455 " --> pdb=" O TRP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 488 Processing helix chain 'C' and resid 497 through 510 Processing helix chain 'C' and resid 511 through 513 No H-bonds generated for 'chain 'C' and resid 511 through 513' Processing helix chain 'C' and resid 540 through 557 Processing helix chain 'C' and resid 558 through 560 No H-bonds generated for 'chain 'C' and resid 558 through 560' Processing helix chain 'C' and resid 577 through 588 Processing helix chain 'C' and resid 600 through 617 removed outlier: 3.660A pdb=" N THR C 617 " --> pdb=" O GLU C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 647 Processing helix chain 'C' and resid 659 through 663 removed outlier: 3.628A pdb=" N GLN C 662 " --> pdb=" O GLY C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 693 Processing helix chain 'C' and resid 703 through 705 No H-bonds generated for 'chain 'C' and resid 703 through 705' Processing helix chain 'C' and resid 722 through 726 Processing helix chain 'C' and resid 739 through 742 removed outlier: 3.629A pdb=" N LEU C 742 " --> pdb=" O GLN C 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 739 through 742' Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.855A pdb=" N MET C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 54 through 61 Processing helix chain 'D' and resid 69 through 74 removed outlier: 3.719A pdb=" N VAL D 73 " --> pdb=" O TRP D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 94 through 108 removed outlier: 3.623A pdb=" N ALA D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 131 Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 177 through 194 removed outlier: 3.538A pdb=" N ILE D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 224 Processing helix chain 'D' and resid 238 through 254 removed outlier: 3.570A pdb=" N GLY D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 306 through 326 Processing helix chain 'D' and resid 348 through 363 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 369 through 374 removed outlier: 4.131A pdb=" N LEU D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 390 removed outlier: 3.649A pdb=" N HIS D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 428 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 452 through 456 removed outlier: 3.589A pdb=" N VAL D 455 " --> pdb=" O TRP D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 488 Processing helix chain 'D' and resid 497 through 510 Processing helix chain 'D' and resid 511 through 513 No H-bonds generated for 'chain 'D' and resid 511 through 513' Processing helix chain 'D' and resid 540 through 557 Processing helix chain 'D' and resid 558 through 560 No H-bonds generated for 'chain 'D' and resid 558 through 560' Processing helix chain 'D' and resid 577 through 588 Processing helix chain 'D' and resid 600 through 617 removed outlier: 3.595A pdb=" N THR D 617 " --> pdb=" O GLU D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 647 Processing helix chain 'D' and resid 659 through 663 removed outlier: 3.641A pdb=" N GLN D 662 " --> pdb=" O GLY D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 693 Processing helix chain 'D' and resid 703 through 705 No H-bonds generated for 'chain 'D' and resid 703 through 705' Processing helix chain 'D' and resid 722 through 726 Processing helix chain 'D' and resid 739 through 742 removed outlier: 3.619A pdb=" N LEU D 742 " --> pdb=" O GLN D 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 739 through 742' Processing helix chain 'D' and resid 743 through 752 removed outlier: 3.873A pdb=" N MET D 747 " --> pdb=" O SER D 743 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 67 removed outlier: 4.619A pdb=" N THR A 22 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 17 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N CYS A 114 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY A 19 " --> pdb=" O CYS A 114 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE A 116 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 21 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL A 162 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N LEU A 338 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 229 removed outlier: 6.330A pdb=" N TRP A 227 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALA A 263 " --> pdb=" O TRP A 227 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE A 229 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR A 202 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR A 294 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 204 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 447 through 449 removed outlier: 6.311A pdb=" N LEU A 402 " --> pdb=" O TYR A 433 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL A 435 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 404 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 593 removed outlier: 5.996A pdb=" N ALA A 591 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASN A 627 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR A 593 " --> pdb=" O ASN A 627 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG A 565 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL A 624 " --> pdb=" O ARG A 565 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE A 567 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ARG A 626 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 569 " --> pdb=" O ARG A 626 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 694 through 695 Processing sheet with id=AA6, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AA7, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 4.639A pdb=" N THR B 22 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 17 " --> pdb=" O ASN B 112 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N CYS B 114 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY B 19 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE B 116 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 21 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL B 162 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N LEU B 338 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 227 through 229 removed outlier: 3.507A pdb=" N TRP B 227 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR B 202 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR B 294 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL B 204 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 447 through 449 removed outlier: 6.266A pdb=" N LEU B 402 " --> pdb=" O TYR B 433 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL B 435 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 404 " --> pdb=" O VAL B 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 591 through 593 removed outlier: 6.048A pdb=" N ALA B 591 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASN B 627 " --> pdb=" O ALA B 591 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR B 593 " --> pdb=" O ASN B 627 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG B 565 " --> pdb=" O GLY B 622 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL B 624 " --> pdb=" O ARG B 565 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE B 567 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ARG B 626 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 569 " --> pdb=" O ARG B 626 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 694 through 695 Processing sheet with id=AB4, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AB5, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.642A pdb=" N THR C 22 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA C 17 " --> pdb=" O ASN C 112 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N CYS C 114 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY C 19 " --> pdb=" O CYS C 114 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE C 116 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 21 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL C 162 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N LEU C 338 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 227 through 229 removed outlier: 6.496A pdb=" N TRP C 227 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ALA C 263 " --> pdb=" O TRP C 227 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE C 229 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR C 202 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR C 294 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL C 204 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 447 through 449 removed outlier: 6.264A pdb=" N LEU C 402 " --> pdb=" O TYR C 433 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL C 435 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE C 404 " --> pdb=" O VAL C 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 591 through 593 removed outlier: 5.966A pdb=" N ALA C 591 " --> pdb=" O LEU C 625 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASN C 627 " --> pdb=" O ALA C 591 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR C 593 " --> pdb=" O ASN C 627 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC1, first strand: chain 'C' and resid 729 through 730 Processing sheet with id=AC2, first strand: chain 'D' and resid 65 through 67 removed outlier: 4.639A pdb=" N THR D 22 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA D 17 " --> pdb=" O ASN D 112 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N CYS D 114 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY D 19 " --> pdb=" O CYS D 114 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE D 116 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU D 21 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL D 162 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N LEU D 338 " --> pdb=" O VAL D 162 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.596A pdb=" N THR D 202 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR D 294 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL D 204 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 447 through 449 removed outlier: 6.266A pdb=" N LEU D 402 " --> pdb=" O TYR D 433 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL D 435 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE D 404 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 591 through 593 removed outlier: 5.897A pdb=" N ALA D 591 " --> pdb=" O LEU D 625 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASN D 627 " --> pdb=" O ALA D 591 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR D 593 " --> pdb=" O ASN D 627 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG D 565 " --> pdb=" O GLY D 622 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL D 624 " --> pdb=" O ARG D 565 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE D 567 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ARG D 626 " --> pdb=" O PHE D 567 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 569 " --> pdb=" O ARG D 626 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 694 through 695 Processing sheet with id=AC7, first strand: chain 'D' and resid 729 through 730 1201 hydrogen bonds defined for protein. 3432 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: 17.75 Time building geometry restraints manager: 12.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 23184 1.03 - 1.22: 56 1.22 - 1.42: 9960 1.42 - 1.62: 13864 1.62 - 1.81: 316 Bond restraints: 47380 Sorted by residual: bond pdb=" C6 ATP A 804 " pdb=" N6 ATP A 804 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.09e+02 bond pdb=" C6 ATP C 803 " pdb=" N6 ATP C 803 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.09e+02 bond pdb=" C6 ATP C 804 " pdb=" N6 ATP C 804 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.09e+02 bond pdb=" C6 ATP B 803 " pdb=" N6 ATP B 803 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.09e+02 bond pdb=" C6 ATP B 804 " pdb=" N6 ATP B 804 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.09e+02 ... (remaining 47375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 84380 3.33 - 6.65: 782 6.65 - 9.98: 124 9.98 - 13.30: 54 13.30 - 16.63: 32 Bond angle restraints: 85372 Sorted by residual: angle pdb=" PB ATP C 803 " pdb=" O3B ATP C 803 " pdb=" PG ATP C 803 " ideal model delta sigma weight residual 139.87 123.24 16.63 1.00e+00 1.00e+00 2.76e+02 angle pdb=" PB ATP B 803 " pdb=" O3B ATP B 803 " pdb=" PG ATP B 803 " ideal model delta sigma weight residual 139.87 123.31 16.56 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PB ATP D 803 " pdb=" O3B ATP D 803 " pdb=" PG ATP D 803 " ideal model delta sigma weight residual 139.87 123.36 16.51 1.00e+00 1.00e+00 2.73e+02 angle pdb=" PB ATP A 803 " pdb=" O3B ATP A 803 " pdb=" PG ATP A 803 " ideal model delta sigma weight residual 139.87 123.36 16.51 1.00e+00 1.00e+00 2.73e+02 angle pdb=" PB ATP D 802 " pdb=" O3B ATP D 802 " pdb=" PG ATP D 802 " ideal model delta sigma weight residual 139.87 123.51 16.36 1.00e+00 1.00e+00 2.68e+02 ... (remaining 85367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 19886 17.65 - 35.29: 1650 35.29 - 52.94: 583 52.94 - 70.58: 250 70.58 - 88.23: 51 Dihedral angle restraints: 22420 sinusoidal: 12540 harmonic: 9880 Sorted by residual: dihedral pdb=" CA GLY C 711 " pdb=" C GLY C 711 " pdb=" N LEU C 712 " pdb=" CA LEU C 712 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLY B 711 " pdb=" C GLY B 711 " pdb=" N LEU B 712 " pdb=" CA LEU B 712 " ideal model delta harmonic sigma weight residual -180.00 -153.48 -26.52 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA GLY D 711 " pdb=" C GLY D 711 " pdb=" N LEU D 712 " pdb=" CA LEU D 712 " ideal model delta harmonic sigma weight residual -180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 22417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2633 0.044 - 0.089: 735 0.089 - 0.133: 210 0.133 - 0.177: 66 0.177 - 0.222: 16 Chirality restraints: 3660 Sorted by residual: chirality pdb=" CB VAL B 587 " pdb=" CA VAL B 587 " pdb=" CG1 VAL B 587 " pdb=" CG2 VAL B 587 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C2' ATP D 803 " pdb=" C1' ATP D 803 " pdb=" C3' ATP D 803 " pdb=" O2' ATP D 803 " both_signs ideal model delta sigma weight residual False -2.68 -2.47 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C2' ATP A 803 " pdb=" C1' ATP A 803 " pdb=" C3' ATP A 803 " pdb=" O2' ATP A 803 " both_signs ideal model delta sigma weight residual False -2.68 -2.47 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3657 not shown) Planarity restraints: 7108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 328 " 0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO D 329 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 329 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 329 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 328 " -0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO C 329 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 329 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 329 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 328 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO B 329 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 329 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 329 " 0.043 5.00e-02 4.00e+02 ... (remaining 7105 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 7409 2.28 - 2.86: 108737 2.86 - 3.44: 131368 3.44 - 4.02: 183180 4.02 - 4.60: 277822 Nonbonded interactions: 708516 Sorted by model distance: nonbonded pdb=" HG SER B 464 " pdb=" O LEU B 466 " model vdw 1.700 2.450 nonbonded pdb=" HG SER D 464 " pdb=" O LEU D 466 " model vdw 1.704 2.450 nonbonded pdb=" OD1 ASP B 590 " pdb=" HH TYR B 754 " model vdw 1.710 2.450 nonbonded pdb=" O LEU A 725 " pdb=" HG1 THR A 729 " model vdw 1.710 2.450 nonbonded pdb=" HG SER C 464 " pdb=" O LEU C 466 " model vdw 1.711 2.450 ... (remaining 708511 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.630 Extract box with map and model: 1.480 Check model and map are aligned: 0.270 Set scattering table: 0.350 Process input model: 82.900 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.009 0.175 24140 Z= 0.629 Angle : 1.217 16.626 32736 Z= 0.839 Chirality : 0.049 0.222 3660 Planarity : 0.006 0.079 4148 Dihedral : 14.683 88.229 9160 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 0.53 % Allowed : 3.23 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3036 helix: 0.19 (0.13), residues: 1324 sheet: -0.03 (0.23), residues: 436 loop : -0.08 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 685 HIS 0.006 0.001 HIS B 453 PHE 0.020 0.003 PHE A 203 TYR 0.015 0.002 TYR A 674 ARG 0.007 0.001 ARG D 564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 621 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7940 (mttp) cc_final: 0.7712 (mttt) REVERT: A 99 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7817 (ttm-80) REVERT: A 444 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7954 (mttm) REVERT: A 597 ASP cc_start: 0.8125 (t0) cc_final: 0.7835 (t0) REVERT: B 66 LYS cc_start: 0.7942 (mttp) cc_final: 0.7725 (mttt) REVERT: B 99 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7812 (ttm-80) REVERT: B 318 MET cc_start: 0.8513 (ttp) cc_final: 0.8311 (ttm) REVERT: B 362 MET cc_start: 0.7415 (mmm) cc_final: 0.7048 (mmm) REVERT: B 597 ASP cc_start: 0.8245 (t0) cc_final: 0.7888 (t70) REVERT: C 66 LYS cc_start: 0.7949 (mttp) cc_final: 0.7732 (mttt) REVERT: C 597 ASP cc_start: 0.8058 (t0) cc_final: 0.7635 (t0) REVERT: D 362 MET cc_start: 0.7510 (mmm) cc_final: 0.7135 (mmm) REVERT: D 597 ASP cc_start: 0.8229 (t0) cc_final: 0.7889 (t0) outliers start: 13 outliers final: 14 residues processed: 630 average time/residue: 2.4820 time to fit residues: 1796.0817 Evaluate side-chains 464 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 450 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 HIS A 483 ASN B 342 GLN B 453 HIS B 483 ASN C 342 GLN C 453 HIS C 483 ASN D 342 GLN D 453 HIS D 483 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24140 Z= 0.289 Angle : 0.597 8.394 32736 Z= 0.314 Chirality : 0.042 0.170 3660 Planarity : 0.005 0.053 4148 Dihedral : 11.614 89.990 3867 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.80 % Allowed : 11.97 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3036 helix: 1.23 (0.14), residues: 1348 sheet: 0.00 (0.22), residues: 464 loop : -0.05 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 685 HIS 0.006 0.001 HIS C 660 PHE 0.015 0.002 PHE C 670 TYR 0.012 0.002 TYR A 385 ARG 0.006 0.001 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 475 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8020 (mttp) cc_final: 0.7779 (mttt) REVERT: A 272 LYS cc_start: 0.7488 (mtpp) cc_final: 0.7241 (mtmt) REVERT: A 360 LYS cc_start: 0.7835 (tppt) cc_final: 0.7559 (tppp) REVERT: A 362 MET cc_start: 0.7586 (mmm) cc_final: 0.7385 (mmm) REVERT: A 444 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7924 (mttp) REVERT: A 597 ASP cc_start: 0.8221 (t0) cc_final: 0.7965 (t0) REVERT: A 714 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7941 (mttt) REVERT: B 66 LYS cc_start: 0.8015 (mttp) cc_final: 0.7772 (mttt) REVERT: B 251 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7205 (ttm110) REVERT: B 362 MET cc_start: 0.7479 (mmm) cc_final: 0.7075 (mmm) REVERT: B 444 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7852 (mttm) REVERT: B 448 GLN cc_start: 0.7913 (tt0) cc_final: 0.7669 (tt0) REVERT: B 693 VAL cc_start: 0.8557 (t) cc_final: 0.8329 (p) REVERT: B 700 PHE cc_start: 0.8530 (t80) cc_final: 0.8241 (t80) REVERT: C 66 LYS cc_start: 0.8129 (mttp) cc_final: 0.7870 (mttt) REVERT: C 597 ASP cc_start: 0.8134 (t0) cc_final: 0.7772 (t0) REVERT: C 678 LEU cc_start: 0.8145 (pp) cc_final: 0.7860 (mt) REVERT: C 693 VAL cc_start: 0.8560 (t) cc_final: 0.8336 (p) REVERT: D 362 MET cc_start: 0.7510 (mmm) cc_final: 0.7124 (mmm) REVERT: D 444 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7854 (mttm) REVERT: D 448 GLN cc_start: 0.7924 (tt0) cc_final: 0.7684 (tt0) REVERT: D 597 ASP cc_start: 0.8258 (t0) cc_final: 0.8027 (t0) REVERT: D 693 VAL cc_start: 0.8564 (t) cc_final: 0.8347 (p) outliers start: 44 outliers final: 24 residues processed: 502 average time/residue: 2.4534 time to fit residues: 1417.5331 Evaluate side-chains 471 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 445 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 714 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 298 optimal weight: 0.5980 chunk 246 optimal weight: 1.9990 chunk 274 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 453 HIS A 483 ASN A 702 ASN B 107 GLN B 453 HIS B 483 ASN B 702 ASN C 107 GLN C 453 HIS C 483 ASN C 702 ASN D 107 GLN D 453 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24140 Z= 0.317 Angle : 0.581 7.886 32736 Z= 0.305 Chirality : 0.043 0.147 3660 Planarity : 0.004 0.056 4148 Dihedral : 11.400 86.947 3857 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.61 % Allowed : 12.99 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 3036 helix: 1.36 (0.14), residues: 1344 sheet: 0.20 (0.22), residues: 476 loop : 0.07 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 685 HIS 0.010 0.001 HIS D 660 PHE 0.015 0.002 PHE A 498 TYR 0.013 0.002 TYR B 674 ARG 0.007 0.001 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 478 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8087 (mttp) cc_final: 0.7818 (mttt) REVERT: A 444 LYS cc_start: 0.8158 (mtpp) cc_final: 0.7941 (mttm) REVERT: A 597 ASP cc_start: 0.8355 (t0) cc_final: 0.8142 (t0) REVERT: A 714 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7992 (mttt) REVERT: B 66 LYS cc_start: 0.8087 (mttp) cc_final: 0.7828 (mttt) REVERT: B 444 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7798 (mttm) REVERT: C 66 LYS cc_start: 0.8138 (mttp) cc_final: 0.7852 (mttt) REVERT: C 256 ARG cc_start: 0.7748 (mtm180) cc_final: 0.7522 (mtm-85) REVERT: C 597 ASP cc_start: 0.8308 (t0) cc_final: 0.8089 (t0) REVERT: C 678 LEU cc_start: 0.8154 (pp) cc_final: 0.7901 (mt) REVERT: D 597 ASP cc_start: 0.8301 (t0) cc_final: 0.8047 (t0) outliers start: 64 outliers final: 31 residues processed: 502 average time/residue: 2.5155 time to fit residues: 1451.6834 Evaluate side-chains 482 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 451 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 714 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 277 optimal weight: 0.9980 chunk 293 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 453 HIS A 483 ASN A 620 GLN A 702 ASN B 104 ASN B 107 GLN B 453 HIS B 483 ASN B 702 ASN C 104 ASN C 107 GLN C 453 HIS C 483 ASN C 620 GLN C 702 ASN D 107 GLN D 453 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24140 Z= 0.264 Angle : 0.547 8.048 32736 Z= 0.287 Chirality : 0.041 0.148 3660 Planarity : 0.004 0.050 4148 Dihedral : 11.166 89.539 3857 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.49 % Allowed : 14.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 3036 helix: 1.49 (0.14), residues: 1360 sheet: 0.17 (0.22), residues: 476 loop : 0.08 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 685 HIS 0.007 0.001 HIS B 660 PHE 0.013 0.001 PHE A 498 TYR 0.010 0.001 TYR A 385 ARG 0.010 0.001 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 458 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8083 (mttp) cc_final: 0.7799 (mttt) REVERT: A 444 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7898 (mttm) REVERT: A 469 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7438 (mptm) REVERT: A 714 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7993 (mttt) REVERT: A 755 ARG cc_start: 0.8136 (mmt180) cc_final: 0.7651 (mmt180) REVERT: B 66 LYS cc_start: 0.8095 (mttp) cc_final: 0.7824 (mttt) REVERT: B 208 MET cc_start: 0.7809 (mtm) cc_final: 0.7600 (mtp) REVERT: B 444 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7748 (mttm) REVERT: C 66 LYS cc_start: 0.8147 (mttp) cc_final: 0.7847 (mttt) REVERT: C 597 ASP cc_start: 0.8279 (t0) cc_final: 0.8070 (t0) REVERT: D 597 ASP cc_start: 0.8303 (t0) cc_final: 0.7989 (t0) outliers start: 61 outliers final: 37 residues processed: 488 average time/residue: 2.5694 time to fit residues: 1447.4964 Evaluate side-chains 492 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 454 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 714 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 250 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 263 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 453 HIS A 483 ASN A 702 ASN B 104 ASN B 107 GLN B 453 HIS B 483 ASN B 702 ASN C 104 ASN C 107 GLN C 453 HIS C 483 ASN C 702 ASN D 104 ASN D 107 GLN D 453 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24140 Z= 0.264 Angle : 0.538 7.959 32736 Z= 0.282 Chirality : 0.041 0.142 3660 Planarity : 0.004 0.052 4148 Dihedral : 11.031 85.695 3857 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.08 % Favored : 97.89 % Rotamer: Outliers : 2.86 % Allowed : 14.26 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.15), residues: 3036 helix: 1.53 (0.14), residues: 1380 sheet: 0.11 (0.22), residues: 476 loop : 0.08 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 740 HIS 0.008 0.001 HIS A 660 PHE 0.012 0.001 PHE A 498 TYR 0.010 0.001 TYR C 385 ARG 0.005 0.000 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 490 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8156 (mttp) cc_final: 0.7856 (mttt) REVERT: A 245 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6402 (mp0) REVERT: A 444 LYS cc_start: 0.8157 (mtpp) cc_final: 0.7898 (mttm) REVERT: A 469 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7452 (mptm) REVERT: A 476 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7095 (mt0) REVERT: A 714 LYS cc_start: 0.8249 (mtmt) cc_final: 0.7992 (mttt) REVERT: B 66 LYS cc_start: 0.8162 (mttp) cc_final: 0.7869 (mttt) REVERT: B 208 MET cc_start: 0.7845 (mtm) cc_final: 0.7642 (mtp) REVERT: B 256 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7306 (mtm-85) REVERT: B 444 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7753 (mttm) REVERT: C 66 LYS cc_start: 0.8161 (mttp) cc_final: 0.7839 (mttt) REVERT: C 245 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: D 245 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: D 362 MET cc_start: 0.7703 (mmm) cc_final: 0.7222 (mmm) REVERT: D 597 ASP cc_start: 0.8307 (t0) cc_final: 0.7936 (t0) outliers start: 70 outliers final: 38 residues processed: 520 average time/residue: 2.4599 time to fit residues: 1473.6191 Evaluate side-chains 514 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 471 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.8980 chunk 264 optimal weight: 0.9980 chunk 58 optimal weight: 0.1980 chunk 172 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 294 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 136 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 453 HIS A 483 ASN A 702 ASN B 104 ASN B 107 GLN B 483 ASN B 702 ASN C 104 ASN C 107 GLN C 157 ASN C 453 HIS C 483 ASN C 702 ASN D 104 ASN D 107 GLN D 453 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24140 Z= 0.210 Angle : 0.517 8.173 32736 Z= 0.272 Chirality : 0.040 0.142 3660 Planarity : 0.004 0.056 4148 Dihedral : 10.761 86.102 3857 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.75 % Favored : 98.22 % Rotamer: Outliers : 2.74 % Allowed : 15.36 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.15), residues: 3036 helix: 1.70 (0.14), residues: 1380 sheet: 0.06 (0.22), residues: 476 loop : -0.06 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 740 HIS 0.005 0.001 HIS A 660 PHE 0.011 0.001 PHE A 203 TYR 0.009 0.001 TYR A 674 ARG 0.008 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 478 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8144 (mttp) cc_final: 0.7845 (mttt) REVERT: A 245 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: A 444 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7880 (mttm) REVERT: A 714 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7992 (mttt) REVERT: B 66 LYS cc_start: 0.8152 (mttp) cc_final: 0.7861 (mttt) REVERT: B 245 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: B 256 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7470 (mtm-85) REVERT: B 444 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7727 (mttm) REVERT: C 66 LYS cc_start: 0.8156 (mttp) cc_final: 0.7828 (mttt) REVERT: C 245 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: C 476 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7269 (mt0) REVERT: D 245 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: D 362 MET cc_start: 0.7672 (mmm) cc_final: 0.7204 (mmm) REVERT: D 476 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7239 (mt0) REVERT: D 597 ASP cc_start: 0.8289 (t0) cc_final: 0.7901 (t0) outliers start: 67 outliers final: 40 residues processed: 508 average time/residue: 2.4495 time to fit residues: 1436.4289 Evaluate side-chains 506 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 460 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 293 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 178 optimal weight: 0.5980 chunk 135 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 483 ASN B 104 ASN B 107 GLN B 157 ASN B 483 ASN B 702 ASN C 104 ASN C 107 GLN C 483 ASN C 702 ASN D 104 ASN D 107 GLN D 157 ASN D 483 ASN D 702 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24140 Z= 0.237 Angle : 0.527 8.058 32736 Z= 0.276 Chirality : 0.041 0.139 3660 Planarity : 0.004 0.054 4148 Dihedral : 10.769 85.695 3857 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.94 % Favored : 98.02 % Rotamer: Outliers : 2.70 % Allowed : 16.26 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 3036 helix: 1.74 (0.14), residues: 1380 sheet: -0.12 (0.22), residues: 444 loop : -0.09 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.007 0.001 HIS D 660 PHE 0.011 0.001 PHE A 203 TYR 0.009 0.001 TYR D 385 ARG 0.008 0.000 ARG B 564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 471 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8158 (mttp) cc_final: 0.7857 (mttt) REVERT: A 245 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6361 (mp0) REVERT: A 444 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7881 (mttm) REVERT: A 714 LYS cc_start: 0.8248 (mtmt) cc_final: 0.8002 (mttt) REVERT: B 66 LYS cc_start: 0.8160 (mttp) cc_final: 0.7867 (mttt) REVERT: B 208 MET cc_start: 0.7873 (mtm) cc_final: 0.7656 (mtp) REVERT: B 245 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: B 444 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7725 (mttm) REVERT: C 66 LYS cc_start: 0.8160 (mttp) cc_final: 0.7834 (mttt) REVERT: C 208 MET cc_start: 0.7696 (mtm) cc_final: 0.7401 (mtm) REVERT: C 245 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: D 245 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: D 444 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7743 (mttm) REVERT: D 597 ASP cc_start: 0.8306 (t0) cc_final: 0.7929 (t0) outliers start: 66 outliers final: 45 residues processed: 507 average time/residue: 2.4057 time to fit residues: 1409.7076 Evaluate side-chains 514 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 465 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 144 optimal weight: 0.0570 chunk 27 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 483 ASN B 104 ASN B 107 GLN B 483 ASN B 702 ASN C 104 ASN C 107 GLN C 483 ASN C 702 ASN D 104 ASN D 107 GLN D 199 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24140 Z= 0.220 Angle : 0.518 8.132 32736 Z= 0.272 Chirality : 0.040 0.138 3660 Planarity : 0.004 0.069 4148 Dihedral : 10.670 85.757 3857 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.09 % Rotamer: Outliers : 2.82 % Allowed : 16.46 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.15), residues: 3036 helix: 1.81 (0.14), residues: 1380 sheet: -0.12 (0.23), residues: 444 loop : -0.06 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 740 HIS 0.006 0.001 HIS A 660 PHE 0.011 0.001 PHE A 203 TYR 0.009 0.001 TYR C 674 ARG 0.012 0.000 ARG C 513 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 476 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8167 (mttp) cc_final: 0.7863 (mttt) REVERT: A 444 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7886 (mttm) REVERT: A 714 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7997 (mttt) REVERT: B 66 LYS cc_start: 0.8166 (mttp) cc_final: 0.7869 (mttt) REVERT: B 208 MET cc_start: 0.7862 (mtm) cc_final: 0.7645 (mtp) REVERT: B 245 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6395 (mp0) REVERT: B 444 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7716 (mttm) REVERT: C 66 LYS cc_start: 0.8151 (mttp) cc_final: 0.7822 (mttt) REVERT: C 208 MET cc_start: 0.7697 (mtm) cc_final: 0.7388 (mtm) REVERT: C 245 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: C 476 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7259 (mt0) REVERT: D 245 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: D 256 ARG cc_start: 0.7612 (mtm-85) cc_final: 0.7206 (mtm-85) REVERT: D 444 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7735 (mttm) REVERT: D 597 ASP cc_start: 0.8303 (t0) cc_final: 0.7920 (t0) outliers start: 69 outliers final: 43 residues processed: 510 average time/residue: 2.4657 time to fit residues: 1451.6024 Evaluate side-chains 519 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 472 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 1.9990 chunk 280 optimal weight: 0.0870 chunk 256 optimal weight: 1.9990 chunk 273 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 272 optimal weight: 0.6980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 483 ASN B 104 ASN B 107 GLN B 483 ASN C 104 ASN C 107 GLN C 483 ASN C 702 ASN D 104 ASN D 107 GLN D 199 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24140 Z= 0.238 Angle : 0.526 8.025 32736 Z= 0.276 Chirality : 0.040 0.137 3660 Planarity : 0.004 0.059 4148 Dihedral : 10.682 85.464 3857 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.08 % Favored : 97.89 % Rotamer: Outliers : 2.57 % Allowed : 17.08 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.15), residues: 3036 helix: 1.82 (0.14), residues: 1380 sheet: -0.11 (0.23), residues: 444 loop : -0.07 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 740 HIS 0.007 0.001 HIS A 660 PHE 0.011 0.001 PHE A 203 TYR 0.009 0.001 TYR C 674 ARG 0.009 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 473 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8167 (mttp) cc_final: 0.7863 (mttt) REVERT: A 272 LYS cc_start: 0.7355 (mtmt) cc_final: 0.7116 (mtpp) REVERT: A 444 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7897 (mttm) REVERT: A 499 GLU cc_start: 0.8477 (mp0) cc_final: 0.8210 (mm-30) REVERT: A 714 LYS cc_start: 0.8288 (mtmt) cc_final: 0.8011 (mttt) REVERT: B 66 LYS cc_start: 0.8168 (mttp) cc_final: 0.7871 (mttt) REVERT: B 208 MET cc_start: 0.7899 (mtm) cc_final: 0.7676 (mtp) REVERT: B 245 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: B 272 LYS cc_start: 0.7372 (mtmt) cc_final: 0.7146 (mtpp) REVERT: B 444 LYS cc_start: 0.8011 (mtpp) cc_final: 0.7720 (mttm) REVERT: C 66 LYS cc_start: 0.8151 (mttp) cc_final: 0.7822 (mttt) REVERT: C 245 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: C 272 LYS cc_start: 0.7361 (mtmt) cc_final: 0.7135 (mtpp) REVERT: D 245 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: D 256 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.7197 (mtm-85) REVERT: D 272 LYS cc_start: 0.7354 (mtmt) cc_final: 0.7126 (mtpp) REVERT: D 444 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7739 (mttm) REVERT: D 597 ASP cc_start: 0.8312 (t0) cc_final: 0.8026 (t0) outliers start: 63 outliers final: 46 residues processed: 506 average time/residue: 2.5725 time to fit residues: 1518.7296 Evaluate side-chains 516 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 467 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.9990 chunk 288 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 136 optimal weight: 0.0980 chunk 200 optimal weight: 1.9990 chunk 302 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 483 ASN B 104 ASN B 107 GLN B 483 ASN C 104 ASN C 107 GLN C 483 ASN C 702 ASN D 104 ASN D 107 GLN D 199 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24140 Z= 0.221 Angle : 0.520 8.056 32736 Z= 0.273 Chirality : 0.040 0.137 3660 Planarity : 0.004 0.063 4148 Dihedral : 10.592 85.509 3856 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.81 % Favored : 98.16 % Rotamer: Outliers : 2.29 % Allowed : 17.44 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3036 helix: 1.87 (0.14), residues: 1380 sheet: -0.13 (0.23), residues: 444 loop : -0.09 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 740 HIS 0.006 0.001 HIS C 660 PHE 0.011 0.001 PHE A 203 TYR 0.009 0.001 TYR C 674 ARG 0.009 0.000 ARG B 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 467 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8173 (mttp) cc_final: 0.7841 (mttt) REVERT: A 245 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: A 272 LYS cc_start: 0.7338 (mtmt) cc_final: 0.7097 (mtpp) REVERT: A 444 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7882 (mttm) REVERT: A 499 GLU cc_start: 0.8520 (mp0) cc_final: 0.8274 (mm-30) REVERT: A 714 LYS cc_start: 0.8260 (mtmt) cc_final: 0.7992 (mttt) REVERT: B 66 LYS cc_start: 0.8171 (mttp) cc_final: 0.7849 (mttt) REVERT: B 208 MET cc_start: 0.7867 (mtm) cc_final: 0.7646 (mtp) REVERT: B 245 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6332 (mp0) REVERT: B 272 LYS cc_start: 0.7349 (mtmt) cc_final: 0.7128 (mtpp) REVERT: B 444 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7712 (mttm) REVERT: C 66 LYS cc_start: 0.8150 (mttp) cc_final: 0.7803 (mttt) REVERT: C 245 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6319 (mp0) REVERT: C 272 LYS cc_start: 0.7337 (mtmt) cc_final: 0.7114 (mtpp) REVERT: D 245 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: D 256 ARG cc_start: 0.7622 (mtm-85) cc_final: 0.7340 (mtm-85) REVERT: D 272 LYS cc_start: 0.7331 (mtmt) cc_final: 0.7110 (mtpp) REVERT: D 444 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7729 (mttm) REVERT: D 597 ASP cc_start: 0.8312 (t0) cc_final: 0.8008 (t0) REVERT: D 678 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7988 (mt) outliers start: 56 outliers final: 42 residues processed: 491 average time/residue: 2.4798 time to fit residues: 1401.9476 Evaluate side-chains 506 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 459 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 681 LYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 222 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 67 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 483 ASN B 104 ASN B 107 GLN B 483 ASN C 104 ASN C 107 GLN C 483 ASN C 702 ASN D 104 ASN D 107 GLN D 199 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.104562 restraints weight = 72769.491| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.74 r_work: 0.2959 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24140 Z= 0.242 Angle : 0.525 7.895 32736 Z= 0.276 Chirality : 0.041 0.137 3660 Planarity : 0.004 0.061 4148 Dihedral : 10.638 85.185 3855 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.11 % Favored : 97.86 % Rotamer: Outliers : 2.57 % Allowed : 17.08 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.15), residues: 3036 helix: 1.95 (0.14), residues: 1372 sheet: -0.11 (0.23), residues: 444 loop : -0.12 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 740 HIS 0.007 0.001 HIS D 660 PHE 0.011 0.001 PHE D 203 TYR 0.009 0.001 TYR A 385 ARG 0.008 0.000 ARG B 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20119.66 seconds wall clock time: 340 minutes 43.32 seconds (20443.32 seconds total)